For what it’s worth, I have this problem sometimes when an album has multiple releases and you can choose which release to pull tags from via the context menu in Picard. There’s also a pretty powerful scripting language that you can use to specify the directory and file re-naming structure as well. It took me a while to get my structure set up properly but once I did it’s been a life saver in keeping my files organized.
If there’s something in particular you’re trying to achieve that’s not working I’d be happy to try and help!