I've tried these methods:

Options Menu -> Pause -> Quit

Options Menu -> Pause -> Play(To check it's paused) -> Quit

In game -> (Spacebar)Pause -> Close game(X button)

All the above methods still gives me (sometimes) Dead Aged Villagers/Totems/More Food/ Increased Tech...etc

The totems can appear anywhere depending on the final skill which has been Mastered but it always appear next to the villager whilst the game is still PAUSED. It's weird!! A non-moving villager with a Totem next to it!