I think it might actually be a problem with the Maritime CS's. The food penalty doubled when I got another ally--I think they may be decreasing your food output rather than increasing it. Just a thought, there might be another explanation.
EDIT: It's not the city-states. I tried DoWing both my maritime allies and the food is still bugged. It's possible that it's not recognizing certain sources of food--I may check that another time. I'll try to look into the code, but I'd appreciate if you could do that as well. I really hope that this is fixed in the current version, because it's a pain to play with.
EDIT #2: I did some testing and here's what I found. The problem wasn't with the food production--that was correct--but with the tooltip. First of all--it double-counted food from some buildings--I had a belief that gave me +2 food from shrines and temples. In the tooltip it showed the shrine/temple giving +2 from buildings and +2 from religion, whereas in the actual growth calculations it was only counted once, as it should have been. Another thing is the maritime city-states: there was a problem but not as I had initally thought. The thing is, the food from the city-states is on the terrain of your city, so it's part of the "food from terrain." However, the tooltip also says that you're getting x food from CS's, even though that food has already been counted on the terrain. In the actual food calculations this isn't a problem but it causes a misleading tooltip.
There was one other problem though. The food output wasn't actually multiplied by the 20% golden age modifier. Turns out that was the only real problem with the food calculations, but it's still a troubling one. However, the tooltip did end up being quite misleading, and if it hasn't been fixed in the current version, I'd recommend looking into it. I'm surprised no-one has found this before.
One more thing. Do you think there's a chance that promotion flags in strategic view will be implemented in an update soon? I think they're a great idea, but as I play the game in strategic view, I can't make too much use of them.