I had problems with Family Guy as well for some reason, and Futurama. I don't know if there are inconsistencies in how many episodes are supposed to be in a season, but it got all the episodes in the wrong order. For example it was stopping season 2 a few episodes early and starting season 3 on the last episodes of S2 In the end I found it best to rename all shows to simply 1x1, 1x2 etc.
Since I started doing that, I have not had any issues just using TVDB. So all my media is now in the format Series name/1x1 etc. With no different folder for series or anything.