I use Mail.app connected to my work's IMAP server. About two weeks ago I noticed that when I moved messages from the INBOX to an Archive folder, or delete the messages, some eventually come back to the INBOX. I haven't been able to catch the moment at which they come back, but they definitely do.
This makes it really hard to get things done as my INBOX is just getting fuller and fuller of mail I've already processed and dealt with. I'm not sure how to diagnose or fix the problem.