Yep. So if I open up the Videos app on iOS, I have The Wire with the number 63 on the top right. I go into that folder and I have all 63 episodes in a row. As mentioned, it probably considers the Complete Series as one giant mega season.
If I go into the iTunes Store and look up the Complete Series, each episode has an iCloud download link. But if I search Season 1 in the iTunes Store, it gives me a $2.99 price tag. So iTunes considers an episode from a season as a different purchase from an episode of a complete series, even if it is technically the same show.
Lastly, if you search for a GoT season that you own, does the entire season give you a price tag? For example, each episode gives me an iCloud download link, but the main page gives me a price instead of a download link.
Right - got you now.
For me, in iTunes, it shows as one folder with each season split up.
It then appears as one long list in the Videos app.
There is a price tag for the whole season, but each individual episode (for my seasons 1-3) says Download.