The problem is precisely that they are not AI cities, and they have governor turned off
Could be automatic placement when population changes, but i keep getting this every turn.
So ok, it's with "experimental" ruleset, but it occured with others, though much more rarely. Seems the biggest the city is, the worse it becomes.
Well, they rarely find a really suitable placement anyway. When production is needed, it looks for food (when prod is low and population can't grow too fast because buildings are missing). When food or trade is needed, it looks for production (and pollutes happily). It does a good job to avoid city disorder, though, even if it's often too close and the slightest change (+1 unhappy) is enough to throw it down.
Seems linked to this topic :
http://forum.freeciv.org/f/viewtopic.php?f=9&t=89863