As you suspect this is caused by periodic scans adding media as its downloaded and plex does not combine these fully when they are added between scans. I think the scanner is just designed to handle addition of media for scenarios like that. So in this example S03E09 was likely the last one downloaded and scanned after the others where scanned and added to plex.
Anyhow, disabling is the best (which is what I do) and then I just manually scan when I want to add stuff.
To fix – you could try a plex dance on the show/season but I’m not 100% sure that will solve it from the recently added view.
BTW… I think there is a feature request to combine these so you could search for that and vote for it.
