I think those broken names/episode numbers are auto-generated from the filenames, then they get sorted wrong. I have the same issue.
One option is to make another library with the old agent and put all the shows that this “upgraded” agent broke into that, but it’s not a great solution.
I’m guessing this will affect any shows not well-maintained on TMDB, or maybe any shows that have divergent season naming on TMDB vs. TVDB. It’s honestly hard to tell what’s going wrong because there’s so little visibility into how the new agent makes decisions, at least from a UI standpoint.
It seems nearly impossible to get the attention of anyone at Plex for anything these days though. There’s currently a major regression in the new agents related to .plexignore, and is probably a single-line diff to a regex somewhere, but…
I recognize that they’re trying to work around the deplorable bait-and-switch profit motivation at TVDB and I support that, just was hoping that there’d be more attention paid to the inevitable bugs as this new agent is pushed out as rapidly as it has been.