If you want to delete the single or selected episodes of a series, there a two methods.
a) Go to episode/Vertical Ellipsis/Get Info/Delete
b) Directly from your storage Directory/ Empty Trash in Plex Library interface.
I hear you about having Auto delete but how would you decipher it is ready for being deleted. What your asking is for a feature. Different criteria for Auto deletion, 24Hr, 48Hr, 7Days, after watching, after watching 75%.