Based on my experience, interim directories like "Season 3" are not required. I don't use them myself.
Believe the incorrect season may be due to using a single-digit SxExx. Have never seen Channels put into the wrong season with SxxExx (both double digits). From my experience, it does not even look at the episode names so am confused how it might place those in the wrong season.
Note you say Channels was putting the episodes in season 5, but their data has them in season 4 (not season 3/5). Was that a typo?
Gracenote shows 8 seasons where the rest of the world shows 6. That said, the six seasons from the rest of the world looks mighty odd. The cause is obvious when you look at the air dates:
Season 1 (everyone): 10 episodes from Nov 21, 2010 - Jan 23, 2010
Season 2a (everyone): 8 episodes from July 24, 2011 - Sep 18, 2011
Season 2b (wikipedia/others): 8 episodes from Feb 14, 2012 - Apr 3, 2021
Season 3 (Gracenote): Feb 14, 2012 - Apr 3, 2021
What non-Gracenote lists as 6 seasons includes seasons (like season 2) that had a five month gap in he middle. Gracenote splits those into discrete seasons whereas other sources keep them together. The wikipedia article includes the non-sensical comment " The season was aired from July 24, 2011 until April 3, 2012 on [History], airing on a weekly basis". (Airing on a weekly basis means something different to me.)
What episodes do you see missing? I did not find anything missing, just in different seasons because of how they handled the odd double-seasons.