I wonder if Atticus Noyle changed Marco's instructions in order to make him kill Eleanor Prentiss Shaw and/or her son instead of Robert Arthur. Probably the Manchurian bosses had changed their mind so they decided to get rid of their troublesome accessary. The reason why Marco aimed at Mr. Arthur at first could be that he was drawn this way and that between the two orders.
No one answered so I might as well give one. No, it was amended due to an understanding between Marco and Raymond. Marco was supposed to shoot at Arthur who was supposed to be standing on the first red star on the floor, but Raymond manipulated Arthur into stepping onto the second red star.
Remember their earlier conversation about having a very deep bond that no one can take away from them? It's this bond that got Raymond subtly signalling Marco to kill him and his mother, instead of Arthur. Marco understood and obeyed, breaking away from the original plan, then after killing the pair, returned to the original plan and followed the rest as normal, like intending to kill himself. Raymond's death was suicide by proxy.
You notice too, at the end, we are in the room with all the Manchurian executives, and they all seem distraught (one of them is openly crying). They definitely didn't intend for Shaw to be killed; he was their golden goose.
"Buy the ticket, take the ride." --Raoul Duke, the great shark hunter