IFF was created for military usage and when civilians use it's function they do it 180 degrees opposite from the way a military would use it.
Since a military can't get the enemy to squawk an identifying code they have their 'friendly" A/C squawk a unique code.
Thus military air defense ignores all codes except the one they are looking for, and they wouldn't give a hoot if a target is squawking the same code used by airliners.
In today's case, with no air war in progress, there would have been no "friendly" code activated, so the SAM crew probably didn't even query the target they were engaging. There was no information for them to find in IFF codes.