As I am not a Plex employee (and more specifically one that works/has worked on the scanner algorithm) I cannot answer that with any authoritative response.
That said, since you do not have the files separated into season folders per the recommended directory structure and your naming is not following the recommended naming, my guess is the scanner is “getting confused” when it goes to do the matching after the season 1 episodes.
The one thing I do know (and this does not directly apply to you since your naming in this case is only working like 95%) is that there have been many posts in the forums over the years regarding matching issues. A good majority of those posts almost always ended up being related to naming conventions not following the recommendation even though it did work at some point.
Basically if you do not follow the recommended naming convention it may work today but there is no guarantee it will not break in a future update to the scanner by Plex.
I do not know if someone that might be able to give you something close to an actual reason might see this thread and be able to respond.
One thing you could do is download your logs and see what the is shown in the “Plex Media Scanner” logs. You might have to initialize a library scan to get the information (depending on how long ago you last scanned) or your might need to do the Plex Dance for it to try and match the files again. But the logs might possible give you clues to why it is not matching.
-Shark2k
