So I'm not sure if this is just a thing I'm experiencing or it's a server thing or this has been answered before or brought up but most of the time when I enter battles I can't switch from the Pokemon I threw out when I click Pokemon it just moves my mouse cursor to the center of the screen, Run just doesn't seem to do anything at all when I click it so I have to /endbattle and if I click Fight or Items I can't back out of the menus I have to click something and I'm really not sure what's up with that.

Do you have JEI installed? That has been known to cause problems.

I do indeed have it I'll get rid of it and see if it fixes it problem.

Edit: It seems to have worked, thanks for the help. Also do you know if NEI items does the same thing or is it any better because honestly a mod where I can see the recipes would be pretty helpful but if neither work I can live with it.

Just remembered NEI needs JEI to work so that kind of answers itself well darn either way thanks for the help I appreciate it.

JEI works fine if you toggle its overlay when you are in battle or some other pixelmon GUI, it defaults to ctrl + o