Was that a neutral city that you took over? If so, those dont level up at all.
Which I've commented on and will repeat here, is stupid.
It makes sense that neutral cities don't level up when they are neutral, even though they're about butt useless and uninteresting because they don't seem to do a damn thing except waste space - yet another simplistically implimented and boring game element. I like the idea of minor powers that aren't trying to win but they could do something other than sit there the whole game. I don't think I've ever seen a neutral/minor sov move - ever.
But, once you take over a neutral city, it is no longer neutral, and it should not be limited to level 1. It makes NO sense and pretty much just encourages the player to raze the POS and build a real city, perhpas in the exact same spot.
I usually just ignore them comletely since they rarely have resources I want and they do serve one good function - they occupy a few spaces on the map that prevent random mobs from spawning. Woot.