Yeah the late game resource generation is completely fucked, and apparently it's even worse on larger maps where it'll generate less total than the amount needed to actually build late game units and projects.

Edit: resources still show up on the map even if you don't know what they are, and you can tell what a deposit is as soon as you're in the right era. It's literally just oil and uranium spawns that are completely fucked, I think because they don't get added until very late. There may be something like it samples X number of spots to place them, and if there's something there it discards the spot from that list but never goes and actually makes sure that a minimum number spawn on the map, so for late game resources it may be trying to generate them under already built districts, deciding those are invalid spawn locations, and just not trying again until it can actually place them (although on a large map it shouldn't be as likely to do that...).