I ran into this with tags in image files, but from ancient times had it happen with audio files too. Wild guesses:
There are several "standards" (sets of fields and schemes) for storing metadata (fields/tags) within files. Different apps might use different fields for the same data, ignoring the other fields that might exist. Other apps might put the same data into multiple fields, or pull it out of multiple fields. Or not. (Deep water to explore all the variations, this is a simplified perspective.)
Possibly the app used to delete tag data blanked it from a field that MC does not use, while the same data still exists in a field that MC does use. (Major pain in photo/image apps/files.)
Or, maybe MC looks at multiple fields that different apps might use to store identical data, then MC grabs from the field that has data rather than a "twin" field that is blank, because usually, the user wants whatever tags exist.
As you mention, there are tools that claim to show ALL fields/metadata in a file, useful to clear up tag mysteries, but sometimes experimentation is needed to determine cause and effect.
I don't have a recent audio file example, but I also use MC to store and manage images. Here is a recent image tags experience, if it helps: Beyond MC I need other apps for image editing/enhancing, such as Google Picasa. But, Picasa mangles any MC tags that have commas in the text (like Lastname, Firstname or City, State). If the image is resaved in Picasa (perhaps after straightening), any commas in tag text are treated as delimiters that create new unwanted tag values, which then show up in MC. Then, deleting those unwanted tag values in Picasa does not reliably delete them from MC, implying Picasa also stores the values in places MC ignores. And sometimes vice versa, deleting the unwanted tags in MC does not banish them from Picasa. (I'm now past that battle; not wanting to avoid Picasa's editing tools, my workaround is to not put commas in image tag text.) I can guess similar craziness could happen when multiple audio tools alter the same file.
I use a cool screensaver to show my photos to family as a random slideshow. I love this app because it allows showing tag text superimposed (and simply positioned and styled via CSS). As a long-time magazine editor, I think captions saying who-what-where-when make photos much more useful, interesting, and fun. The screensaver app will show any/all tag fields I desire, because the developer knows there are any possibilities. I've found that some apps see the field Caption as an alias for field Description, but some apps see them as separate fields, and often one is blank while the other has text. Some apps use yet another field name for similar info. Crazy!
The obvious safe path is to use only one tool to edit (tagging is editing) files, but not always feasible.