This is not entirely uncommon due to versioning. The network TV version might have aired in a different order from the later released DVD boxset, or the US version aired in a different order than the EU version, etc. Instead of refreshing metadata, try using the Identify option. Under each of the results it will show the source, so pick the one that matches the episode order you want.
I have a lot more indexers than that, and not much better luck. You really need a private torrent tracker if you want to automate books. Every few years I look into a way to automate it more like movies & TV with just usenet and public trackers, but every few years I don’t turn up much. I have Readarr running, but it rarely finds anything except the most mainstream bestseller type results. Just doing things manually with something like Anna’s Archive or Libgen is really the only thing that works well. Results for comics work better, but I can’t stand Mylarr’s interface, so have always just manually done that too when I have the urge.