According to the commentators Houdini had more impressive wins and the game that decided the tournament (the third game shown in this article) was supposed to b

According to the commentators Houdini had more impressive wins and the game that decided the tournament (the third game shown in this article) was supposed to be a draw but somehow got blundered away due to the contempt rule. Basically it was very close and Houdini may actually be slightly better, especially at the abstract heuristic stuff. Although Houdini creates good positions for itself, Stockfish excels at brute force and somehow always manages to turn things around as it transitions into the endgame.