Yup, we're aware of this:
http://www.slitherine.com/forum/viewtop ... 0&start=20
It might be something to address when we get around to a new patch (along with other issues, such as the S key crash), but in the meantime:
"Hmm that is some strange behavior indeed. It's not particularly harmful, but it's certainly not intended. City hexes with no flags may see a change because of this, but perhaps not.
Trying to milk prestige out of this would undoubtedly be more trouble than it's worth (needing so many level bombers+requirement for enemy unit to be present+time constraints+weather restraints)."