Happened to me as well. It was due, for me, to having gotten a bunch of messages at once ... I got a new spell ... research completed ... and a scout I had all got attacked at once when I ended my last turn.
The first two windows (spellbook and research) came up, but the combat box never popped for the scout getting mauled by a big wolf, so the game refused to let me continue because it was waiting (I assume) for feedback from the scout.
I had to destroy the unit for the game to progress.