If you mean raw *.aac files, that's probably where the issues lie. There is no native tagging system for ADTS AAC, although some players/taggers allow "welding" ID3 tags in which may or may not be compatible with other players. This can be solved by wrapping the AAC files into a M4A wrapper, which allows regular MP4 tagging.
I do the majority of my tagging through external taggers like Kid3 and Mp3tag which have easy options to delete all tags. You can delete tags in MB with Tag Inspector but chances are it won't find any in the AAC--at least it didn't when I tried adding a cover image to an AAC via Mp3tag and checking it in MusicBee--because of adherence to standards. Anyway, I recommend you check out one of the above mentioned taggers.
After stripping, you can wrap the AAC in a M4A wrapper with ffmpeg.exe using the following command line executed within a folder containing just the problem AAC's you wish to wrap:
FOR %F IN (*.aac) DO C:\ffmpeg\ffmpeg.exe -i "%F" -codec copy "%~nF.m4a"
Change the path of ffmpeg to match yours. After the M4A wrapper is applied, you can tag it easily with MusicBee. The wrap process is lossless. You could try wrapping them as-is without stripping and then seeing if they can be cleaned up later (ID3 removed, etc) but the results would be anybody's guess.