So as I said in comments section, trying to enable habitats on moons. There is issue with parent planet. If planet has megastructure then can't build anything on moons.

It seems that parameter has_megastructure applies not only to moon but also for parent planet.
So if I disable this condition then multiple habitats can be built on single body.

This is not a problem for player. I can just ignore that and not build more then 1 habitat. However AI does not care about that. And this causes next issue: if AI has multiple habitats in the same place, you can't or at least it's very hard, to select every habitat to invade it with army.

At this point I reenabled this condition and just build habitats on moons first, before building it on parent planet. No idea how to solve it (if possible at all) at the moment.