I've had some success recovering from a stuck/confused board when playing on a level against the A.I. as follows:
1) make sure the placement of the pieces on your board agrees with the placement shown in the app. Don't worry if lights are blinking on the board
2) select pause&exit (not just pause, and certainly not quit) in the app
3) turn your board off and then on again
4) select play against AI in the app and select Resume play of the paused game
Hope this works for others
Is there a way to load the previous firmware?