@wythagoras Difficult. If it's not from the question author, flag, that's noise. If the question author says thanks, at least don't flag while the comment is young. The asker thanking the answerer isn't noise per se, so give it time to reach the answerer. If it's an old "thanks" (from the OP), flag or not, your call.
@DanielFischer Also, do you sometimes experience the following bug: When viewing vote counts on a deleted question, the score changes instead of showing vote counts?
@wythagoras That's mostly not a bug. When the score of a post changes due to the deletion of an account or invalidation of votes, the score is not automatically updated. It's updated when certain actions occur, namely when somebody votes on that post or splits the vote count. For deleted posts, of course voting on the post isn't possible. So when you split the vote score on a post whose score has changed since the displayed score was last updated, the score changes.
What may be a bug is that sometimes the split is not shown/immediately collapses again. But it's not a big deal, click on the score again and it splits fine.