NCAA Rule 7, Section 3, Paragraph 2

I. Quarterback who is not outside the tackle box, and is attempting to save yardage, intentionally throws a desperation forward pass that falls incomplete where there is no eligible receiver. Ruling: Intentional Grounding. Penalty: Loss of down at the spot of the foul. The clock starts at the snap.

My guess in this case was that the refs did not feel he was throwing a desperation forward pass to avoid a loss of yardage, but rather was throwing the ball as high/long as possible to run clock.