There seems to be a couple of issues with imported files.
1 - If a title has a ? in it, it seems to mess things up. See here:
2 - Channels doesn't seem to like folders with titles other than 'Season X'. See here where Season 6 was split into two parts and the scanning of the imported TV show folder hasn't found these folders.
Having removed the ? and consolidated Season 6 into a single folder called Season 6, both issues have been resolved. Note the 'ghost' of the old episode 3 that previously had a ? in its file name. Channels knows it should have a ? in its real name though so it is displayed correctly within Channels.
This looks like a samba issue so I guess you're importing from an SMB mount?
Settings > Local Content > Maintenance > 
> Prune Deleted
Yes, correct it is on my NAS.
Thanks, it's easy enough to tidy it up. I was just noting it to highlight that it is corrected having removed the '?'
