Ive had this happen sporadically and unfortunately i have already ended my turn but i wanted to mention it as it seems related to some other pathfinding issues we've encountered.
The situation was I had an army in forest waiting to get on a dock which was covered by 2 NPC medusas. I ran out of moves in the forest but had a 6pack of elves behind them. so i pointed the elves to the medusas and they went there. i got an out of sync and then reloaded and they were gone. the medusas remained and i killed them the next turn with my other army.
Interestingly enough I lost another army in similar fashion attacking a city adjacent to a dock. It was against flash in the same game. It seems to be something to do with docks and passing over stacks that the game doesnt like. this isnt as bad as the beta 2 bug that caused the original out of syncs but still kind of strange.
just thought id mention it since im already all over the forums today. might as well do all my posting at once