CatGarfield
Chieftain
I think this may have been a result of unrest. Even when a city is gifted, then there is a number of turns of unrest equal to the population. During this time, no are generated by the city, though happiness buildings will contribute , and trade routes will produce . However, the city still generates during this time.
After reading this I had to go and check, although I was pretty sure that enough time had passed (around 20 turns is quite a bit for a size 3 city to be in resistance). Plus I checked all the other yields and it's definitely "the bug". The city center tile yields (food, production, gold) are NOT added, but everything else is.