The door should have been flashed before masonry was installed. To rely upon caulk after the fact is lazy and just plain wrong. As you said there is nothing to prevent moisture running down the house wrap, behind the brick mould and into the door cavity. The fact that it has leaked from day one is a testament it was done incorrectly from the start. Despite his defensiveness I'd ride him to fix it correctly, NOT just throwing caulk at it. Sounds like he might want to kick the can down the road until the warranty runs out.