Very occasionally, on Meta, I'll see a flag count in my header bar, like so:
I then click on this, and my 10k toolbar will show something like this:
I've actually had this happen quite a few times, and finally remembered to take a snapshot.
My guess is that the number is for flagged comments, but since I'm not a mod I can't see the comments, so there is some glitch showing me the mod flag count.
The tooltip text says
We have posts flagged for moderator attention, perhaps you can help