The album art finder, that does its thing when new files are added to the main music library, does not like it when folders are mixed in with single tracks. My songs are in a "folder/folder/musicfolder1/musicfile.flac", "folder/folder/musicfolder2/musicfile.flac" and "folder/folder/musicfile.flac" hierarchy. When musicbee scans "folder", if it digs down to musicfolder/musicfile, it marks album art correctly (whether there is or isn't). When musicbee also sees some loose files after it finishes scanning "musicfolder"s, it goes insane and assigns random album art from unrelated folders (that as far as I can tell have zero relationship to that file), regardless of whether those files already have embedded artwork or not.
How I discovered this bug is that
1)if you move those unrelated album art pictures elsewhere, it keeps the artwork assigned to those files but complains that it can't find the pictures anymore when one opens the tag editor and, most importantly,
2) regardless of whether the artwork was moved or not, if the "embed artwork in the music file" sync option is selected, musicbee throws a formerly mysterious "Exception of type 'System.OutOfMemoryException'" message when one attempts to sync those files, which is what I was trying to troubleshoot for way too long.
Rescanning the library fixes nothing; the workaround for 1) is to delete everything from the library and reimport. Those music files that don't have their own folder still get assigned random album art but at least now musicbee knows where that random art is and stops complaining about it. This does nothing for 2) however. As far as I can tell the only way to fix that is to select any other option in the "artwork storage" menu in the sync settings.