MC currently uses LAV filters to parse the playlists on the disc. It defaults to the longest playlist or the one with the best/most audio tracks which is usually good for movies because they are usually the longest thing on the disc and have the best audio tracks (ie DTS-MA or TrueHD).
This is suboptimal for discs of TV episodes because they have somewhere between 3 and 6 episodes per disc of roughly the same duration and similar audio tracks. Although quite often the slightly longest episode is the season opener ie. episode 1 which is why MC has by default chosen this to play.
You can right click and choose a different title to choose a different episode. However they will only be listed by length in the menu, so you cannot know for certain which episode is which.
You can also add the episodes separately in your library using the 'Stacks'/'Particles' feature.
How I do it:
I rip the bluray/DVD into a folder structure on my HD (Video__TS for DVD and BDMV for bluray).
In the MC library, right click on the file and go to Stacks->Particles->Auto-particle DVD/Bluray (or whatever it is called - I'm not home at the moment).
This gives you particles of the different playlists on the disc in the library (which are basically new library entries for the same data that you can edit separately)
Make sure each of the particles are 'tagged' with Media Subtype (Tv Show), Series (Justified) and Season (1). I just highlight them all and change the tags in one go. Change the episode tag to whatever you think appropriate. There may be some trial and error here.
Then select them all and do a 'Get TV/Movie info..'
They should then get the correct metadata.
A bit longwinded, but actually doesn't take that long to do. Note that you need to rip into a folder structure for this to work - it won't work for iso.
Hopefully sometime in the future we can get some java menu support for MC in which case the episodes will be automatically tagged.