In regards to the 2 point conversion in SB XLIV, the VP of Officiating come the following explanation:

"By rule, when a receiver with possession of the ball is in the act of going to the ground and performs a second act by reaching out to break the plane, that completes the process of the catch and the ball is dead when it breaks the plane."

Still doesn't help it sit right, but I guess they will make sure to enforce this everytime in the future.