Your first city should always start with 30 population, but every city after that will only start with 3. The only thing that will give your cities more population is time, with prestige determining how many people you get a turn. If your very first city doesn't have 30 population when your sovereign founds it, that's a bug. Also, if Altar's second (or third, or...) city has more than 3 population the turn it's founded, THAT'S a bug.
