Just want to mention that I have the same problem (random episode missing with multiple multi-episodes within a season) and the “random episode” which is missing is different with different orders of addition of multi-episodes.
Naming convention has been respected.
If somebody seriously wants to hunt down this bug, I am happy to produce some more details and logs. I will be unavailable due to traveling during the next couple of days, but I am happily assisting somebody who wants to analyze the cause.
This is a relatively recently introduced bug, so don’t try to guide me through database integrity speculations and plex dance trivia. These are not causing (or fixing) the issue.
Of course, every reasonable developer could just add a couple of multi-episode files to the same season in order to try to replicate. 
P.S.: It looks like some kind of indexing problem.
