Solved -..

Update to 1.12.2 and it will be fine, you won't regret

 

1.12 PvP is so bad. And I'm pretty sure that won't fix the problem

 

I'm pretty sure that updating to the latest version with fixed bugs, exploits and better performance is much better than using nearly 4 year old dinosaur

 

I can only guess, without looking further. But I believe IPortal v1.5 is the issue. If you look, at the very end of the error that plugin occurs. Throughout the crash its all about entities going through portals. My guess, something or someone went through one of these "IPortals" and the plugin must not be able to properly read it, which results in the crash. I HIGHLY suggest deleting the IPortal plugin, restarting your server and seeing if that fixes it.

 

If you need something to replace IPortal try this : https://www.spigotmc.org/resources/bungeeportals.19/

 

I recommend Bungeeportals instead of IPortal, also.. If you don't like 1.12 because of the PvP I suggest using https://www.spigotmc.org/resources/oldcombatmechanics-disable-1-9-hit-cooldown.19510/

Good luck!
- G1lles