I'd like to suggest that when "private" actions are taken, perhaps the issue history can mention that they were private? For example, one of the bug reports has, "2004-12-15 12:29 codemastr Note Added: 0008634" in the history. This not was marked as private. However, a user went to that bug and noticed the history said a note was added. But, then noticed that no such bugnote was visible. Therefore, I've received several bugnotes asking if there is a bug regarding the displaying of bugnotes. I think something like "Private Note Added" would make it much better. The same holds for relationships. If you add a relationship to a bug that is marked as private, the history should indicate this.

Ideally, it'd be nice if the issue history only displayed the "private" entries to those who have access to see them. If that's not possible, then having it inform the user they are private is a good idea.