I will look at the actual numbers a little closer, but I must have gone 5-6 turns without seeing that city get it's 1 pop remaining. For some reason it seems stuck right now. Thought I would post this as a possible bug (seems like a rare one though).
It happens when you have multiple cities, and prestige that is not even with 50.
Lets say you have 3 cities, one of them with 2 grain, and 25 food per grain (just enough for levelling to level 2, as shown above).
If you have 3 prestige, each city will grow at 1 population each turn, and even the 3rd with only 2 grain will become level 2.
but if you have 4 or 5 prestige, they will grow at a respective 1.3 population, or 1.6 population each turn, and it ends up getting clogged up around 49 population. If it cannot add THE FULL GROWTH, it will not add anything at all.
Sincerely
~ Kongdej