This depends on what the RO saw. If the RO saw the two hits on Alpha on the target as the shooter fired them, then it's "obvious to the RO which two holes were shot." If the RO did not see the hits and misses as they were fired but absolutely saw only three shots on target and it has four holes, that's a mandatory reshoot as the target cannot be scored as shot because the alphas may not belong to that competitor.
It is not correct, if you didn't see the actual hits, to assume the alphas belong to the competitor, and if you're absolutely certain there were only three shots (you don't mention if the RO confirmed this... or could...), it's a reshoot.
Otherwise, if the RO wasn't counting shots, it's two alpha. If the shooter wants to appeal to the RM, score the COF, pull the target, replace it, call the RM and next shooter to the line.