Yep, even if the clock has stopped, when the ball is snapped, the clock starts again, so it's running, you can spike the ball. Total BS call on the refs, just one of quite a few questionable decisions they made in that game.
In order for Winston to spike the ball, the ref had to spot it and turn possession over to the center. It was their job to tell the center and Jameis at that time that the clock was stopped.
That isn’t favoring the Saints, that’s telling the player what the ruling on the field is, which the refs are REQUIRED to do.