Disable the “automatic” library scan for a while and trigger it manually, after you have made sure that all new files have been transferred to the media storage completely.
I remember such a behaviour when the library scan is triggered and a partly uploaded/copied file is being scanned and has its hash value computed.
Since many MKV files look the same when you only look at their file headers (and compute its hash), the server might mistake each partly uploaded file as the same episode.
To clear this wrong hash from Plex’s database, you will need to perform the complete Plex Dance with each involved episode file.
