In the first Julio César Chávez vs. Meldrick Taylor fight, Taylor was winning pretty conclusively. Then, with 17 seconds left in the fight, he was knocked down (video). He got up in time, but with 3 seconds left in the fight, the ref signaled that Taylor was unable to continue, and Chávez was declared the winner by TKO.
This shocked me, because common sense dictates that if the ref hadn't stopped the fight, it would have ended before anything else could happen: By the time that the fighters returned to the middle of the ring and the ref said "fight", the bell would have rung. Thus, Taylor was deemed "unable to defend himself" when there was no need for him to defend himself, because Chávez didn't have time to throw another punch.
On the other hand, we have the Lucian Bute vs. Librado Andrade fight. Notwithstanding the fact that Bute was in terrible shape by the time the fight ended, and the fight really should have been stopped before then (he was literally falling from one side of the ring to the other), the fight ended in an exactly opposite manner from the Taylor - Chávez bout. Bute was knocked down with seconds left in the fight, and although the count was obscenely long (about 20 seconds long), and although the fight ended before he got up, he was up within about 9 seconds of the knockdown (video).
In this case, Bute won the fight.
So we have two very different outcomes - both of which were highly controversial - from similar circumstances.
What is supposed to happen in cases like this? One fighter is in very bad shape, and if it happened in the middle of a round, the ref would have to stop the fight to keep him from taking more damage. However, the fight is basically over, and there is no chance that he will actually take any more damage. What is the ref supposed to do? Ignore the fact that the fight is basically over, and base his decision solely on the fighter's condition? Or ignore the boxer's condition, because the fight is basically over?