From what I can tell it is assumed that the play was taken to replay because the official said that the ball didn't cross the goal line when Holmes caught. It is then assumed that he meant that when the ball touched Holmes' hands, it was out of the endzone.
The two main criticisms of this are that a) there isn't enough evidence to conclusively say that the ball crossed the plane of the goal line and that b) the official, Coleman, misinterpreted the rule by stating that it was a touchdown because the player had both feet down in the end zone when he gained possession of the ball (or something to that effect). But what if his explanation, word for word, was the correct reason to overturn the call on the field?
I think there is a good chance (not positive, it's just a guess) that the play was taken to replay for a different reason than what most people assume. The official may have called Holmes down outside of the end zone because he didn't think Holmes had two feet down when the ball made contact with his hands. He then thought that Holmes' got two feet down after his momentum carried him outside of the end zone. In this scenario, the replay would have been used to determine if Holmes had two feet touching the ground when the ball made contact with his hands, not whether the ball was across the goal line when it touched his hands.
The replay shows fairly conclusively that Holmes did have both feet down when he caught the ball. If this was what was in question for the official who made the call on the field, then this would be pretty easy to overturn. It would also explain why the official who reviewed the play only mentioned Holmes' feet, and not whether the ball crossed the goal line, during his explanation. If the official who made the call on the field thought that the ball had crossed the goal line when Holmes gained possession, then it really doesn't seem like there is enough evidence to overturn that. Therefore, really the only issue is whether both feet were down, which seems like a pretty easy call on replay.
This may not be why the play was called to replayed, but it seems like a possibility that nobody is really discussing.