Drop the extra letters… it’s not s01e01a, s01e01b… but s01e01 and s01e02…
Plex is only going by the sXXeYY pattern… if you have 2 files containing s01e01, Plex will treat both of them as different versions (duplicates) of episode 1 of season 1.
As for docker – in my view you just added an unnecessary level of complexity to your setup.