Please take the steps to reproduce as a grain of salt.
*Accepted new skirmish battle
*going to My Turns and opened other still running skirmish battle
*it started loading the map, but I was on the opposite side of the team
*I restarted the program in hard mode... without saving and opened the existing battle and then all was fine
I guess I had something similar before, where I started a skirmish battle and entered an existing scenario game and the troops where strange deployed. Maybe it has something to do, when you accept a new challenge and then start another match (not the new one), while the accepted fight has the status, waiting for other player. But I'm not sure.

Hope this description helps.