Yeah, it's probably just the 4.0 AI still being broken. I think it's going to be a while before it works as well as 3.14. To give a more specific guess...
At least as of 3.99 (the last time I played on observer), a lot of the starting conditions were still broken depending on origin/civic/ethic combinations, sometimes running several resources on a deficit. I wouldn't be surprised if a lot of combos are still on razor thin margins, particularly some of the bad ones you get with rando empire generations. Players can figure this out, at least partially by using trade, but the AI might possibly still be having trouble with it, leading some empires to spend 15 years trying to fix their economies rather than expanding.
What difficulty are you observing on, OP? If you're seeing this on higher difficulties, this probably isn't the cause, as the AI gets increasingly large subsidies to their economies.