Whenever I create settlers and have them join my cities, about half of the time, the cities population doesn't increase. Could someone please explain?

You have to create the settlers in another city, not in the same where are you building the settler. Every time you build a settler, the pop for that city will be reduce in 2 or 1 (if you have a republican gob). If you build a settler and the make him join the same city nothing will happen.

also a city of population 31 won't increasewhen you add settlers to it.