This reply here should apply to your use case as well:
https://www.filebot.net/forums/viewtopic.php?f=8&t=11930#p51281


Generally works now, but 3x03 may not yet have existed at the time of processing in your case:
$ filebot -rename *.mkv --db TheTVDB -non-strict --action TEST --log INFO
[TEST ...

Hey all

I've been having an issue with a particular episode that is being matched to a completely different season and I can't seem to figure out why.
Through the UI, specifically selecting the show seems to match correctly however via the command prompt below, not so much.

Filebot Version: 4.9.1 ...