I am still experiencing this issue with just pixelmon installed. I tried slowly removing all of my other mods one by one to see which was causing it and at the end, with only pixelmon left, it still keeps happening. What I did notice was, that it mainly seems to happen when I tried to quickly shift click a lot of pokemon into the PC. It does not happen every single time, it took me a few attempts each time of shift clicking 5 pokemon from my party into my PC. The Pc box i was trying to shift click them into was also almost full, with only the 5 spaces where I wanted to shift click said pokemon into remaining.
crash log: https://pastebin.com/cjTqSiqh