And this example is about as bad as it gets:

It got the title correctly, but it wasn't able to pick up on the proper season number for some reason, even though the "0048" was part of a "word" in the title and not isolated by whitespace. I've also seen Filebot get confused when there are isolated numbers, like years or sequel numbering. It seems like any kind of numerics in the title throw it off.
Also notice that it doesn't consistently pick the right or wrong season. The pattern seems random as to whether it chooses Season 1 or Season 2.
For additional background: I ran my "Anime" pre-set:

Hope this helps track down the issue.