Take a real close look at how your filters are set up. Make sure that there aren’t any conflicts, i.e., multiple filters snagging a message. If multiple filters can snag the same message, it is hard to predict where it will end up.

Pay particular attention to any e-mail messages that ended up in the wrong folder. There is always a reason as to why something like this happens. Sometimes something very subtle can snag a message and put it into a particular folder.

You will very likely find that Thunderbird is acting logically.