I looked into this a bit more because I was starting to experience it myself. Here is what is going on:
Plex recently changed their EPG source away from Gracenote to something much more inferior (Rovi, I think?). With this change, many more shows are missing S##E## information as the guide just does not have it available. When that happens, Plex will name the file something like ShowName-AirDate-Title instead of ShowName-S##E##-Title.
For whatever reason, the Regex engine in MCEBuddy is breaking when it detects the first format. Not only does the Regex not work (even though it should), but it prepends regex to the title, and basically it all just takes a huge dump. I have no idea why this happens (I suspect a bug in the application), and I submitted a bug report, but unfortunately no one has responded, and I have no idea if they ever will.
I decided to take matters into my own hands and write a PowerShell script to monitor my MCE folder for files that matched a Regex pattern, then I’m renaming them before MCEBuddy detects they are there so that MCEBuddy’s native metadata matching works again. If you are interested in this script or instructions, let me know.
My hope is that the application is corrected in a future release so that this is no longer necessary, but for now, it’s the best solution I have been able to come up with.