Everytime I refresh my library in XBMC both Thor and The Avengers are part of The Avengers Collections....this is honestly getting annoying.

Yes, it is. Sorry about that. Some users keep moving Thor and others back to The Avengers Collection, despite the collection guidelines. This issue will get fixed. There is a ticket being worked on that will add the ability for mods to lock collections (to keep stuff like this from happening).

Also, I think there's a bug with Thor right now which I do not have the ability to fix. It says it is part of The Avengers Collection but it does not show up in The Avengers Collection, therefore I do not have the ability to move it back to Thor (MCU series) at the moment until travisbell or someone else looks at it.

I have fixed up Thor and added it back to the Thor Collection.