Not picking up some content and misnaming/labeling others

That can lead to the problem you are seeing.

Kenichi The Mightiest Disciple - s00e01

That looks correct.

Are your files MP4? If so, they ma have a different name in the embedded title field. If you’ve set PMS to use this, then renaming the file won’t matter, it will just use this embedded title.

Also, renaming files doesn’t change what PMS thinks it is. You need to perform the Plex Dance on these files.