game does not save automatically at times. I would que up some pirates at the tavern and it would give me 15min wait so I log off and come back later. I log back in to find that pirates were not even made. I would have to reque the pirates again. This tends to happen a lot. Also happens with upgrades. I would upgrade before bed but when I come back on the next morning upgrade did not happen. So game is not saving when logging off.
This has luckily never happened to me, but its indeed a big problem. Have you tried reinstalling the app maybe? What device are you playing on? Maybe @Chris [Midoki] can help you out.
Don't worry there have been a few players reporting this over the last few days, and we know what it is. The fix is currently being tested and will be in the next update