Oct 8 2018
I've switched to a different version of AWB and it seems to have corrected the issue.
Oct 4 2018
I'm not having this issue with Referata or Wikipedia though, I'm able to login to those sites but not Miraheze, which lead me to believe it was Miraheze related, I will check with reporting the bug to the people who work on AWB if it's purely AWB related.
Aug 7 2018
Thanks for the help :)
Oh, sorry I figured it out, they're still on the wiki, it's just as I've reordered some of the articles the names been changed by the bot. Sorry for wasting your time.
They didn't come from Wikimedia Commons, so I guess it means it's a MediaWiki bug, does this mean I need to reupload them or will they comeback on their own?
Jun 25 2018
Ok understood, thanks for the update.