It sounds like you encountered a situation that's described in this answer in our Support FAQ.

The best and safest way to pause the game when you're not going to play it for awhile is to press the space bar, which immediately pauses the game, then quit the game. Leaving it running, even if it's paused, leaves it vulnerable to issues caused by power failures, computer crashes, etc. It's best to quit the game when you're not actually playing it, with the game speed set to something appropriate for how long you expect to be away from it.