Create a "master bubble sheet" with all bubbles marked according to the correct answers.
Set up an array of LEDs on top of the "scanner" with a photodiode underneath each bubble.
Since the answer sheets are marked deep black with a No 2 pencil no light should penetrate the bubble containing the correct answer. If the wrong bubble is filled the correct bubble will be exposed to light causing the software to reduce points.
Aligning master and answer sheet only correct answers leave the photodiodes unexposed to light.
Even multiple answers can be evaluated using that design (line 6).
I think you're proposing a hardware solution to something that should properly be done by software. What if they want to change the layout of the answer sheet?