I think this is somewhat related to the unplayable board bug of the previous version, where using a skill that changes colors can cause a board with no matches.
I think I was using Iron Fist, and while my board was still playable, the gems flashings to suggest a move still was where it was before using the skill, but it was no longer a valid match.
When checking for a dead board to reshuffle, you also should check to see if the hinted match is still valid.