I found a glitch while encoding some TV episodes the other day - the application reads (or at least appears to read) S##E## out of the filename to establish the appropriate details, but this only seems to work if the series and episode numbers are <99.
Some stuff is organised on TVDB with series numbers corresponding to year (for example, standalone BBC documentaries are like this, so, for example "The Deadliest Crash The Le Mans 1955 Disaster" is "S2010E25"). Additionally, while not common, some TV series have a lot more than just 99 episodes in them. Mostly this seems to be the Specials stuff (For example the show "Tabletop" is now up to S00E206) but it does happen elsewhere too (to use BBC Documentaries again, the documentary "Rik Mayall Lord Of Misrule" is "S2014E273").
This can cause problems as either it won't be able to find the episode or mis-identify it (S00E206 would pull up metadata for S00E20 for example). You can work around it using the "Season" and "Episode #" fields under "Video"