Unless you install some 3rd party tool, Windows does not read metadata from flac files.
(That's probably not true anymore, I believe W10 has full flac support these days)
So your File Explorer displays the filenames, and MusicBee shows titles that are in the metadata.
You probably have some files that have a mismatch between their filename and the title tag.
You could also use the 'filename' column in MusicBee, or use the 'Title' column in File Explorer.