I think a popup would be annoying and get in the way. A better option might be to highlight in some way (perhaps via a change in text color) items that you have flagged, so you can easily see that you may have made a mistake.

Ditto I have accidently flagged 12 submissions without noticing (but no comments). This is in addition to the many times where I've noticed an accidental flagging and immediately unflagged it. In my case, it's entirely a consequence of reading HN on a phone.