After upgrading to 3.11.10 from 3.2.23 these kind of stack traces started appearing on console:

[18616.401828] WARNING: CPU: 1 PID: 1977 at net/ipv4/tcp_output.c:1061 tcp_fragment+0x32e/0x340()
[18616.401866] Modules linked in: xt_nat netconsole configfs xt_multiport xt_recent xt_state dummy cmac af_key crypto_null hmac sha256_generic sha512_generic rmd160 xcbc cbc des_generic cast5_avx_x86_64 cast5_generic cast_common blowfish_x86_64 blowfish_generic blowfish_common serpent_avx_x86_64 serpent_sse2_x86_64 serpent_generic camellia_generic camellia_aesni_avx_x86_64 camellia_x86_64 twofish_x86_64_3way twofish_x86_64 xts twofish_generic twofish_common ctr deflate zlib_deflate iptable_filter iptable_nat nf_conntrack_ipv4 nf_defrag_ipv4 nf_nat_ipv4 ah4 esp4 ipcomp xfrm_ipcomp xfrm4_tunnel tunnel4 xfrm_user xfrm_algo xfrm4_mode_tunnel xfrm6_mode_tunnel authenc iptable_mangle sch_htb sch_sfq pptp gre l2tp_ppp pppox l2tp_netlink l2tp_core sha1_ssse3 sha1_generic arc4 ecb ppp_mppe ppp_generic slhc xfrm4_mode_transport tun cls_u32 xt_REDIRECT nf_nat nf_tproxy_core xt_tcpudp xt_conntrack nf_conntrack xt_NFLOG nfnetlink_log iptable_raw ip_tables xt_hashlimit ip_set_hash_ip xt_set ip_set nfnetlink xt_time x_tables loop joydev x86_pkg_temp_thermal hid_generic coretemp kvm_intel kvm usbhid hid crc32_pclmul crc32c_intel ghash_clmulni_intel aesni_intel ablk_helper tpm_tis snd_pcm cryptd lrw tpm hpilo mperf evdev tpm_bios snd_timer snd gf128mul soundcore glue_helper aes_x86_64 hpwdt snd_page_alloc microcode pcspkr lpc_ich psmouse serio_raw button mfd_core processor acpi_power_meter ehci_pci ext4 jbd2 mbcache crc16 sd_mod crc_t10dif ahci uhci_hcd libahci ehci_hcd libata usbcore scsi_mod tg3 usb_common libphy ptp pps_core thermal thermal_sys
[18616.402934] CPU: 1 PID: 1977 Comm: openvpn Tainted: G        W    3.11.10 #2
[18616.402971] Hardware name: HP ProLiant DL320e Gen8, BIOS J05 12/10/2012
[18616.402995]  0000000000000425 ffff88020b423938 ffffffff814afecc 0000000000000425
[18616.403049]  0000000000000000 ffff88020b423978 ffffffff8105e277 ffff8801f27f8b80
[18616.403109]  ffff8801f101e080 0000000000000060 0000000000000020 ffff8801f5a311c0
[18616.403167] Call Trace:
[18616.403187]  <IRQ>  [<ffffffff814afecc>] dump_stack+0x49/0x5d
[18616.403226]  [<ffffffff8105e277>] warn_slowpath_common+0x87/0xb0
[18616.403252]  [<ffffffff8105e2b5>] warn_slowpath_null+0x15/0x20
[18616.403276]  [<ffffffff81417b1e>] tcp_fragment+0x32e/0x340
[18616.403301]  [<ffffffff8140f475>] tcp_mark_head_lost+0x1a5/0x2d0
[18616.403326]  [<ffffffff8140f5f0>] tcp_update_scoreboard+0x50/0x80
[18616.403351]  [<ffffffff81412984>] tcp_fastretrans_alert+0x5d4/0xae0
[18616.403376]  [<ffffffff814148ce>] tcp_ack+0x6ee/0xf10
[18616.403402]  [<ffffffff8144aba2>] ? _decode_session4+0x2c2/0x2e0
[18616.403428]  [<ffffffff81415a4c>] tcp_rcv_established+0x2cc/0x810
[18616.403456]  [<ffffffff8141e955>] tcp_v4_do_rcv+0x255/0x4f0
[18616.403481]  [<ffffffff81420399>] tcp_v4_rcv+0x609/0x760
[18616.403506]  [<ffffffff813fc5c0>] ? ip_rcv+0x350/0x350
[18616.403530]  [<ffffffff813f56c5>] ? nf_hook_slow+0x75/0x160
[18616.403554]  [<ffffffff813fc5c0>] ? ip_rcv+0x350/0x350
[18616.403578]  [<ffffffff813fc68e>] ip_local_deliver_finish+0xce/0x250
[18616.403604]  [<ffffffff813fc858>] ip_local_deliver+0x48/0x80
[18616.403629]  [<ffffffff813fbee9>] ip_rcv_finish+0x119/0x360
[18616.403653]  [<ffffffff813fc4a3>] ip_rcv+0x233/0x350
[18616.403678]  [<ffffffff813c890e>] __netif_receive_skb_core+0x5fe/0x7a0
[18616.403705]  [<ffffffff813c8ad2>] __netif_receive_skb+0x22/0x70
[18616.403729]  [<ffffffff813c8c23>] process_backlog+0x103/0x200
[18616.403755]  [<ffffffff813c944a>] net_rx_action+0x10a/0x280
[18616.403779]  [<ffffffff8106309f>] __do_softirq+0xef/0x280
[18616.403805]  [<ffffffff814bdd1c>] call_softirq+0x1c/0x30
[18616.403827]  <EOI>  [<ffffffff81015815>] do_softirq+0x65/0xa0
[18616.403864]  [<ffffffff813c74e8>] netif_rx_ni+0x28/0x30
[18616.403891]  [<ffffffffa03e101f>] tun_get_user+0x31f/0x860 [tun]
[18616.403917]  [<ffffffff81010000>] ? perf_trace_xen_cpu_write_gdt_entry+0xf0/0xf0
[18616.403958]  [<ffffffffa03e1655>] tun_chr_aio_write+0x85/0xa0 [tun]
[18616.403985]  [<ffffffffa03dfe4f>] ? tun_chr_aio_read+0x9f/0xb0 [tun]
[18616.404012]  [<ffffffff8117b53a>] do_sync_write+0x7a/0xb0
[18616.404036]  [<ffffffff8117b7c8>] ? rw_verify_area+0x58/0xe0
[18616.404061]  [<ffffffff8117b918>] vfs_write+0xc8/0x170
[18616.404085]  [<ffffffff8117be6a>] SyS_write+0x5a/0xa0
[18616.404110]  [<ffffffff814bc469>] system_call_fastpath+0x16/0x1b
[18616.404134] ---[ end trace 96c92912ac0c5c66 ]---

Setting /proc/sys/net/ipv4/tcp_fack to 0 resolves the issue but I'm not sure if that's the way to go, better if this gets fixed :)
These warnings appear if there's much TCP load on the server and if that load is related to the tun interface. They're the same every time they appear so there's no point in pasting multiple stack traces. OpenVPN version is 2.3.0, running in TAP mode and operating the tun device.
The good thing is that this kind of TCP load used to make the server panic under 3.2.23 kernel with a similar stack trace to this one:

[7400083.464717] skb_over_panic: text:ffffffff812e6800 len:848 put:512 head:ffff8801e27ed800 data:ffff8801e27edd30 tail:0x880 end:0x680 dev:<NULL>
[7400083.464783] ------------[ cut here ]------------
[7400083.464806] kernel BUG at net/core/skbuff.c:207!
[7400083.464828] invalid opcode: 0000 [#1] SMP
[7400083.464855] CPU 1
[7400083.464861] Modules linked in: mii dca netconsole configfs xt_recent xt_RAWNAT(O) compat_xtables(O) ip6_tables dummy xt_multiport xt_state af_key crypto_null hmac 
sha256_generic sha512_generic rmd160 xcbc cbc des_generic cast5 blowfish_x86_64 blowfish_generic blowfish_common serpent camellia twofish_x86_64_3way twofish_x86_64 two
fish_generic twofish_common ctr deflate zlib_deflate iptable_filter iptable_nat ah4 esp4 ipcomp xfrm_ipcomp xfrm4_tunnel tunnel4 xfrm_user xfrm4_mode_tunnel xfrm6_mode_
tunnel authenc iptable_mangle sch_htb sch_sfq pptp gre l2tp_ppp pppox l2tp_netlink l2tp_core sha1_ssse3 sha1_generic arc4 ecb ppp_mppe ppp_generic slhc xfrm4_mode_trans
port tun cls_u32 ipt_REDIRECT nf_nat nf_conntrack_ipv4 nf_defrag_ipv4 nf_tproxy_core xt_tcpudp xt_conntrack xt_NFLOG nfnetlink_log iptable_raw ip_tables xt_NOTRACK nf_c
onntrack xt_hashlimit ip_set_hash_ip xt_quota2(O) xt_set ip_set nfnetlink xt_time x_tables coretemp crc32c_intel ghash_clmulni_intel acpi_power_meter hpwdt hpilo tpm_ti
s tpm tpm_bios aesni_intel snd_pcm snd_timer snd soundcore snd_page_alloc cryptd aes_x86_64 aes_generic psmouse evdev pcspkr joydev serio_raw button container processor
 ext4 mbcache jbd2 crc16 sd_mod crc_t10dif usbhid hid uhci_hcd ahci libahci libata scsi_mod tg3(O) ptp pps_core ehci_hcd usbcore thermal usb_common thermal_sys [last un
loaded: 3c59x]
[7400083.465717]
[7400083.465736] Pid: 32445, comm: openvpn Tainted: G           O 3.2.23 #1 HP ProLiant DL320e Gen8
[7400083.465783] RIP: 0010:[<ffffffff8129da7f>]  [<ffffffff8129da7f>] skb_put+0x7a/0x89
[7400083.465825] RSP: 0000:ffff88020ae23a80  EFLAGS: 00010286
[7400083.465848] RAX: 0000000000000099 RBX: ffff8801117bc800 RCX: 0000000049be49be
[7400083.465884] RDX: 0000000000000000 RSI: 0000000000000046 RDI: 0000000000000246
[7400083.465920] RBP: ffff8801e27436c0 R08: 00000000000000bd R09: 0000000000bd0004
[7400083.465956] R10: 00000000ffffffff R11: 0000000000000000 R12: ffff8801e27436e8
[7400083.465992] R13: ffff8801292db240 R14: ffff88010caff000 R15: 00000000000000b0
[7400083.466029] FS:  00007f5338955700(0000) GS:ffff88020ae20000(0000) knlGS:0000000000000000
[7400083.466066] CS:  0010 DS: 0000 ES: 0000 CR0: 000000008005003b
[7400083.466089] CR2: 0000000004522000 CR3: 00000001f693d000 CR4: 00000000001406e0
[7400083.466125] DR0: 0000000000000000 DR1: 0000000000000000 DR2: 0000000000000000
[7400083.466161] DR3: 0000000000000000 DR6: 00000000ffff0ff0 DR7: 0000000000000400
[7400083.466197] Process openvpn (pid: 32445, threadinfo ffff8801ecc80000, task ffff8802006783c0)
[7400083.466235] Stack:
[7400083.466253]  0000000000000880 0000000000000680 ffffffff814de165 ffff8801117bc800
[7400083.466303]  ffff8801e27436c0 ffffffff812e6800 ffff880100000200 ffff8801117bc8e8
[7400083.466351]  ffff8801117bc908 0000015000000003 ffff8801117bc908 ffff8801117bc800
[7400083.466400] Call Trace:
[7400083.466419]  <IRQ>
[7400083.466443]  [<ffffffff812e6800>] ? tcp_retransmit_skb+0x291/0x58b
[7400083.466468]  [<ffffffff812e6cff>] ? tcp_xmit_retransmit_queue+0x195/0x231
[7400083.466493]  [<ffffffff812e3643>] ? tcp_ack+0x18ad/0x1a89
[7400083.466517]  [<ffffffff812e17fe>] ? tcp_validate_incoming+0x68/0x255
[7400083.466541]  [<ffffffff812e3ddb>] ? tcp_rcv_established+0x5bc/0x68d
[7400083.466567]  [<ffffffff812eb228>] ? tcp_v4_do_rcv+0x1bd/0x3ee
[7400083.466592]  [<ffffffff812ec896>] ? tcp_v4_rcv+0x450/0x6fe
[7400083.466616]  [<ffffffff812cfba5>] ? T.1004+0x4f/0x4f
[7400083.466641]  [<ffffffff812a9355>] ? napi_skb_finish+0x1c/0x31
[7400083.466666]  [<ffffffff812cfce2>] ? ip_local_deliver_finish+0x13d/0x1aa
[7400083.466691]  [<ffffffff812a8e9d>] ? __netif_receive_skb+0x452/0x496
[7400083.466715]  [<ffffffff812a8fcd>] ? process_backlog+0xec/0x1c7
[7400083.466739]  [<ffffffff812a991a>] ? net_rx_action+0xa8/0x207
[7400083.466764]  [<ffffffff8104f1b2>] ? __do_softirq+0xc4/0x1a0
[7400083.466789]  [<ffffffff81097ac9>] ? handle_irq_event_percpu+0x166/0x184
[7400083.466814]  [<ffffffff8136dcec>] ? call_softirq+0x1c/0x30
[7400083.466839]  [<ffffffff8100fa3f>] ? do_softirq+0x3f/0x79
[7400083.466863]  [<ffffffff8104ef82>] ? irq_exit+0x44/0xb5
[7400083.466886]  [<ffffffff8100f38a>] ? do_IRQ+0x94/0xaa
[7400083.466909]  [<ffffffff8136676e>] ? common_interrupt+0x6e/0x6e
[7400083.466932]  <EOI>
[7400083.466955]  [<ffffffff8136ba92>] ? system_call_fastpath+0x16/0x1b
[7400083.466979] Code: 8b 57 70 48 89 44 24 10 8b 87 e0 00 00 00 48 89 44 24 08 8b bf dc 00 00 00 31 c0 48 89 3c 24 48 c7 c7 d9 1a 50 81 e8 0f 6d 0c 00 <0f> 0b eb fe 89 c0 48 83 c4 28 49 8d 04 00 c3 41 57 


Otherwise, without the tun interface involved, the warning cannot be observed, nor was there any kind of a panic by the kernel in the 3.2.23 version. I guess these two, the panic and the warning are related.

Here's the stack trace of 3.12.4:

[  344.928972] WARNING: CPU: 1 PID: 2048 at net/ipv4/tcp_output.c:1065 tcp_fragment+0x32e/0x340()
[  344.929711] Modules linked in: xt_nat netconsole configfs af_packet xt_multiport xt_recent xt_state dummy cmac aesni_intel aes_x86_64 crc32c_intel af_key crypto_null sha1_ssse3 sha256_generic sha512_generic rmd160 xcbc cbc des_generic cast5_avx_x86_64 cast5_generic cast_common blowfish_x86_64 blowfish_generic blowfish_common serpent_avx_x86_64 serpent_sse2_x86_64 serpent_generic camellia_generic camellia_aesni_avx_x86_64 ablk_helper cryptd camellia_x86_64 twofish_x86_64_3way twofish_x86_64 glue_helper lrw xts gf128mul twofish_generic twofish_common ctr deflate iptable_filter iptable_nat nf_conntrack_ipv4 nf_defrag_ipv4 nf_nat_ipv4 ah4 esp4 ipcomp xfrm_ipcomp xfrm4_tunnel tunnel4 xfrm_user xfrm_algo xfrm4_mode_tunnel xfrm6_mode_tunnel authenc iptable_mangle sch_htb sch_sfq pptp gre l2tp_ppp pppox l2tp_netlink l2tp_core ipv6 arc4 ecb ppp_mppe ppp_generic slhc xfrm4_mode_transport tun cls_u32 xt_REDIRECT nf_nat xt_tcpudp xt_conntrack nf_conntrack xt_NFLOG nfnetlink_log iptable_raw ip_tables xt_hashlimit ip_set_hash_ip xt_set ip_set nfnetlink xt_time x_tables loop joydev hid_generic usbhid mgag200 ttm drm_kms_helper drm gpio_ich pcspkr i2c_algo_bit i2c_core psmouse tpm_tis hpilo tpm tpm_bios hpwdt serio_raw lpc_ich ehci_pci rtc_cmos ipmi_si ipmi_msghandler evdev acpi_power_meter button ext4 jbd2 mbcache crc16 sd_mod ahci libahci libata scsi_mod tg3 ptp pps_core uhci_hcd ehci_hcd thermal
[  344.939748] CPU: 1 PID: 2048 Comm: openvpn Not tainted 3.12.4 #3
[  344.940755] Hardware name: HP ProLiant DL320e Gen8, BIOS J05 12/10/2012
[  344.941762]  0000000000000429 ffff88020b423928 ffffffff814de004 0000000000000429
[  344.942788]  0000000000000000 ffff88020b423968 ffffffff81060287 ffff88020b4239c8
[  344.943816]  ffff8800eaf10000 0000000000000180 0000000000000100 ffff880200302a00
[  344.944852] Call Trace:
[  344.945869]  <IRQ>  [<ffffffff814de004>] dump_stack+0x49/0x5d
[  344.946919]  [<ffffffff81060287>] warn_slowpath_common+0x87/0xb0
[  344.947959]  [<ffffffff810602c5>] warn_slowpath_null+0x15/0x20
[  344.949013]  [<ffffffff8148366e>] tcp_fragment+0x32e/0x340
[  344.950062]  [<ffffffff8147af95>] tcp_mark_head_lost+0x1a5/0x2d0
[  344.951110]  [<ffffffff8147b110>] tcp_update_scoreboard+0x50/0x80
[  344.952070]  [<ffffffff8147e1dd>] tcp_fastretrans_alert+0x65d/0xab0
[  344.952658]  [<ffffffff81480485>] tcp_ack+0xad5/0x1180
[  344.953279]  [<ffffffff812f490c>] ? add_interrupt_randomness+0x3c/0x190
[  344.953867]  [<ffffffff8148148c>] tcp_rcv_established+0x2cc/0x810
[  344.954461]  [<ffffffff8148a4e5>] tcp_v4_do_rcv+0x245/0x4e0
[  344.955053]  [<ffffffff8148bef6>] tcp_v4_rcv+0x5f6/0x750
[  344.955644]  [<ffffffff81467f10>] ? ip_rcv+0x3a0/0x3a0
[  344.956236]  [<ffffffff81460f85>] ? nf_hook_slow+0x75/0x160
[  344.956817]  [<ffffffff81467f10>] ? ip_rcv+0x3a0/0x3a0
[  344.957414]  [<ffffffff81467fc2>] ip_local_deliver_finish+0xb2/0x230
[  344.957969]  [<ffffffff81468188>] ip_local_deliver+0x48/0x80
[  344.958521]  [<ffffffff814677e9>] ip_rcv_finish+0x119/0x360
[  344.959073]  [<ffffffff81467dff>] ip_rcv+0x28f/0x3a0
[  344.959622]  [<ffffffff81433ffe>] __netif_receive_skb_core+0x5fe/0x7a0
[  344.960176]  [<ffffffff8101c2c9>] ? sched_clock+0x9/0x10
[  344.960726]  [<ffffffff814341c2>] __netif_receive_skb+0x22/0x70
[  344.961306]  [<ffffffff8143431b>] process_backlog+0x10b/0x210
[  344.961848]  [<ffffffff81434b5a>] net_rx_action+0x10a/0x280
[  344.962392]  [<ffffffff810653bf>] __do_softirq+0xff/0x2d0
[  344.962936]  [<ffffffff814e48dc>] call_softirq+0x1c/0x30
[  344.963476]  <EOI>  [<ffffffff81016395>] do_softirq+0x65/0xa0
[  344.964020]  [<ffffffff81432c28>] netif_rx_ni+0x28/0x30
[  344.964567]  [<ffffffffa04a0464>] tun_get_user+0x314/0x830 [tun]
[  344.965148]  [<ffffffffa04a0a75>] tun_chr_aio_write+0x85/0xa0 [tun]
[  344.965683]  [<ffffffff8117487a>] do_sync_write+0x5a/0x90
[  344.966204]  [<ffffffff81174af8>] ? rw_verify_area+0x58/0xe0
[  344.966710]  [<ffffffff81174c48>] vfs_write+0xc8/0x170
[  344.967199]  [<ffffffff8117523a>] SyS_write+0x5a/0xa0
[  344.967670]  [<ffffffff814e3247>] tracesys+0xdd/0xe2
[  344.968124] ---[ end trace d8bbaf64668174aa ]---

As you can see, the same stuff again. I guess the problem is in the tcp_mark_head_lost somewhere, the kernel issues a warning because (packets - oldcnt) * mss  is greater than skb->len.