This has happened to me numerous times. I get a Total Destruction in the last seconds of the fight, the message 'Total Destruction' is displayed just as the clock runs out but I only get awarded 2 stars and not the full 100%.
Yes, have had the same many times. But have been told it was to do with the difference between the your device and the servers registering that last kill and the win by the time the clock runs out. Usually only happens in the last second or two. I thinks its more of the 'nature of the beast', rather than a bug. On the other side I have also seen my games go on for 5-10 sec after the 3 minute window showing me a win (in-game). But the server still only allows 2 stars and whatever was taken before the true clock ran out.