I had this happen twice. When you play a game on one device (in my case my phone) and then pick up to play on a different devices (ie. Mac or iPad), sometimes (I have not figured out when) the cloud syncs a syncs the version of the game that has been last accessed on the second device, overwriting the progress done.
When I go back to my phone, on launch it re-syncs with the older version causing all progress made in the meantime to be lost.
So for example Game Center’s achievement still shows that I have a win, whereas the game does not show it.