This is when the officials should be allowed to explain their decisions after the match, rather than locking themselves away. Nobody other than them still knows what caused the ref to change his mind twice.
From highlights, unofficial videos and photos, my take on it is this:
1. Neither the ref nor linesman thought it was a corner or a penalty, else the linesman would have pointed to the corner flag or held his flag across his chest.
2. The goal kick was taken from inside the 6 yard box, and the ball was not moving, so no problem there.
3. There were players in the box when the goal kick was taken. While opposition players should not be in the box, a retake should only happen if they interfere with the goal kick. This didn't happen so no issues here.
4. The ball was a couple of inches inside the area when Ruffels first touched it. This should have resulted in a retake. However, at full speed, that would have been very difficult to spot, especially from the linesman's point of view. And, that split second was hardly likely to affect what subsequently happened.
From that, I can only conclude that the linesman was worried about the number of players in the box, and that the ref then spent a few minutes clarifying the rule with his assistants, to eventually give the correct decision on that particular point.