As far as I understand, the Flight Termination System is safed before the landing burn. It's more dangerous to have it potentially still active after landing. So at this point it can't blow itself up anymore.
Until the last moment it also doesn't target the barge itself, but slightly to the side. Only very shortly before landing does it correct the target to the actual landing position. So in most cases it would simply hit the water instead of anything else when there is a major issue.
If you watch the livestream for yesterday's falcon heavy launch on youtube the second camera angle is a rendering showing trajectory, and you can actually see the center core adjusting closer and closer to the droneship with each step as it gets more confident that it's able to land safely.
Until the last moment it also doesn't target the barge itself, but slightly to the side. Only very shortly before landing does it correct the target to the actual landing position. So in most cases it would simply hit the water instead of anything else when there is a major issue.