Some questions:
* Are you using a single-file TW or a nodeJS installation?
* What plugins have you installed?
* What tags are being automatically added (i.e., are they special "system" tags, or your own tags)?
* Do they get added to every tiddler you edit, even if those tags weren't there before... or is it just not deleting tags that already existed on the tiddler being edited?
-e