I recently started up a server, and I have noticed that several of my players keep getting a bug that says "Waiting..." when they are fighting a Pokemon. And other players have stated that they aren't able to press "Back" after clicking their bag or trying to select a Move.

With the "waiting..." glitch, which is a bit more common, one player reported that before he threw the ball or selected the move, the Pokemon would disappear from in front of him, and it would just vanish.

Is there any way to fix this issue? If it's something I might be doing wrong, I'm open to any suggestions :)

Thank you for your time!

The bag/battle button issue is caused by them using JEI. Let them know they should remove it. See here for more information: http://pixelmonmod.com/wiki/index.php?t ... ities_List.
As for the waiting bug, it depends. Can be caused by JEI or other mods. Please provide a list of all plugins on your server, with the versions, as well as an extended description of how to reproduce the bug. We cannot fix what we cannot reproduce.