With Herbert costing his team opportunities to score is a pattern and it has nothing to do with scheme and philosophy.
I did not religiously follow Herbert, but I saw enough to know some QBs make mistakes with Herbert it seems to be a pattern. Here are some exmaples.
Throwing the ball 10 yards out of the end zone on the final play against Auburn is not a mistake, it's just piss-poor play by Herbert. I would expect every HS QB to put that ball in the end zone and Herbert is a 5th year senior. It suggests to me that when the game is on the line Herbert might get a little too hyped up or nervous to execute effectively.
I watched him play the next week against Nevada. If only Herbert could play against Nevada every week.
Next game I turned in was right before the half against Washington. Oregon has the ball at Washington 34 with :08 left in game. Herbert escapes pocket and rolls left burning the time left on the clock before throwing into the end zone...correction, throwing the ball about 2 yards out of the end zone to the left of a WR who would have had an opportunity to make the catch. No time left on clock to attempt a FG.
Then in the Rose Bowl, 4th quarter 10 minutes left down 27-21, ball on Wisconsin 35, 3rd and 2...Herbert escapes pocket and rolls left, reverses trying to run to the right and gets sacked. Oregon forced to punt. That was an easy read for him to throw the ball away before reversing course which would have resulted in a 4th and 2 with the option to go for it or attempt a FG.
Those are the types of plays that don't have anything to do with schema and philosophy, but an inability to make the right play, the smart play that costs the team from being in a position to score to keeping the team from the opportunity to score.