Well, funnily enough I do own a Captured Neanderthal City that Had 2 pop and it's initial ring around the city, I've noticed that the Neanderthal focusses on a few of it's cities, while practically leaving others, example, the city I captured had like 10 units in it, but the two next door (Including the one I want to capture saves me a settler), had combined less, so I'd guess Somewhere what you did to change it worked, in a quirky way that wasn't intended, I'll go boot up the game and check in world edit the various Neanderthal cities and report back
Okay, just checked, and It's interesting, the Reason the Neanderthal and Barbarian cities don't grow beyond 1 pop, and some Do is all to do with how much Food it can produce before it switches to building Units, so Probably the best way to fix the overbuilding of units would be to program the AI to build Culture or something else then units, because Food is getting used to build units, so Some cities grow while others are stagnant, in the end it's just Location that defines things, and the amount of soldiers is just tied to how much turns it takes for 1 unit
but bottom line, Neanderthals Can't grow above max 2 because all their food goes to units,
I am unsure about Barbarians, because my game isn't that far, all AI don't possess Writing and I'm about to get to the Third age, Sorry forgot to note the exact date, but it's around 5000 BC towards AD