Bret won becuase he was in the middle of a push and, for a few months during that push, was the WWF champion. But why should the champion win matches and cleanly at that? They should all be screwy finishes I suppose.
As for Austin, Bret did not beat Austin every time they faced each other. Austin beat Bret by DQ at In Your House: Revenge of the Taker and then beat the shit out of Bret the following night on Raw in a streetfight. Besides that, the finishes of those matches always kept both men strong.