So far I am only noticing this problem for my show Alaska: The Last Frontier, but I am sure it happens a lot to different shows.
My idea to fix this is to have Sonarr recognize the episode it grabbed for manual searches and then rename download to that episode it was downloaded for.
The problem is that when I download the episode that I know is correct it has the incorrect episode number in the name. When Sonarr processes the episode it uses the incorrect episode number and either replaces good existing episode or puts it with wrong episode number and shows incorrect episode as downloaded and of course the wrong episode will play on your media player i.e. Plex.
Example:
Available download = Alaska.The.Last.Frontier.S04E14.HDTV.x264-KILLERS
Actual episode it is for = Episode 15