Renaming issue with episode numbers
See the selected file in the screenshot below. This file is actually episode 1 and special 2 of Ghost in the Shell 2nd GIG So the episode number should have been: 01-S02 This applies to all files of GITS SAC and GITS 2nd GIG
GITS Arise also has episode number issues because some files are connected to both GITS Arise and GITS Arise alternative architecture. This can be seen in the top 2 files in the screenshot below Might be better in this case to only mention multiple episode numbers within the same series

Could be an issue your with your renaming script but I think the issue is that we currently lack the ability to link the same file to two different episodes.
Don't see how it could be a problem with my renaming script since %enr is the tag for the episode number. I can't change it any further then that
I do see the files in question on multiple episodes as the episode number suggests.

Oh fuck it's been a year. Fine I'll fix it
Was this fixed @da3dsoul
Could be an issue your with your renaming script but I think the issue is that we currently lack the ability to link the same file to two different episodes.
I don't know about the renamer scripts, but we technically support linking manual files to multiple episode entries (in the v3 api) as long as the episodes are listed on anidb (and made available locally).
And i mean multiple episodes from different series.
I don't remember, but a lot has changed there