Seen this several times also. Rotating is different than not seating. If the impression coping is not seated before the impression, it will not be at the correct vertical height and may also be rotated. If at the correct vertical height and only rotated, it is seated but the impression coping was not positioned in the impression the right way. The only real way to be sure what happened is to take a new impression and compare the two models. If different vertical height the doctor did may not have it seated. If just rotated then the lab did not re-position the impression coping correctly.
open tray impression eliminates this. If the doctor insists on a closed tray suggest a more rigid PVS impression or a Poly ether impression to allow a more accurate and rigid positioning of the impression coping back in the impression.
Many impression copings (nobel replace, nobel conical) will not allow the impression coping to engage or screw in at all unless they are seated so many doctors feel it is not necessary to take an xray to verify seating of the impression coping, Each system is different and you just have to try the impression coping on the analogue to see if is possible to engage the screw without the hex or trilobe engaging.
Last possible cause is that the implant is not integrated and in fact rotated after the impression was taken, yes I have seen this happen