Hundley finished 27-for-42 with 320 yards with two interceptions. Jonathan Franklin ran for 110 yards on 25 carries.
The Bruins (3-0), have now run up 115 points in their first three games.
David Piland threw 60 passes for the Cougars, but he only completed 28 of them and had the five picks.
Houston is off to an 0-3 start after going 13-1 last season.
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