You might try putting this in the PCB section of the forum.
I don't use Altium, but is is possible you put that rectangle in the soldermask or maybe a copper layer on accident? I notice there's no white line in the rectangle; there is a white line in all the other holes. Also, you can't mill a perfect rectangle. You need to radius the corners, and if your radius is too small, there may be an extra charge for swapping tooling.
Each manufacturer has a default smallest radius they use for routing, without swapping bits to a smaller bit (which cuts slower, wears out faster, and potentially breaks more frequently).