When a player click moves too quick in a battle, it MAY cause battle go stuck and go to the state of waiting.
This issue also occurs in some other conditions, no matter who are you having a battle with, but I'm not sure about the exact conditions of this issue.
Also it seems work well in client.

Another issue is when you try to catch a pixelmon in a battle and have already thrown a ball(may throw very quick? It need to be proved because someone said that he clicked the button one by one but it still happened), the next turn if you choose to throw a ball, you MIGHT automatically throw a random ball instead of choosing one.

I don't know whether there's a connection between the two issues, so I put them together, in case that they may be caused by battle sticks and operation mistakes.
And these issues do not occur very frequently, and can't be triggered constantly.
Hope that you could solve these issues breezily~ :)

Also some players said that the 2nd issue would occur even they didn't choose to throw a ball in next turn. The ball will automatically be thrown in the next turn even they do nothing.
I guess that these issues have something to do with threads in server, since it hardly occurred in client.
Hope this information will help you to solve the problem.

Thanks for the reports. We were able to reproduce the last two issues (finally! took a while) and have made an internal ticket for them. The first one may be tied to it, but feel free to open a new ticket if a future fix doesn't resolve that. Keep an eye on the ticket status!

This should be fixed for the upcoming version. Closing!