I finished a game yesterday, getting all the tech levels, the puzzles, and reaching 90 villagers. I reopened it just now and was greeted by a message saying "Congratulations! You have reached the third population milestone of 50 villagers". Thing was, I had 89 villagers at the time. One had died while the game was closed.

I'm pretty sure the "50 villagers" message appeared at the normal time when I was building up the population; I am certain that the "90 villagers" message appeared yesterday.