Is there a way I can remove a teacher's letter of recommendation from my app?

I asked 3 teachers for a letter of rec. UPenn only allows 2 teachers so I did not tell my science teacher that I am applying to UPenn but on the Common App, it says that he submitted the letter for UPenn. I think it is because he sent it through Naviance and that shows all of the schools I am applying to. I wanted my math teacher and latin teacher to write my letters for that school. What should I do? Should I ask him to cancel his letter? That would sound very rude though. I don’t think he particularly likes me so that is why I chose my math and latin teachers. But honestly I am not close with any of my teachers so they probably sound all the same.

Talk to your GC on Monday.

On the Common App, you can assign individual teachers to each college. That way, you can just choose not to send his rec.

I talked to my gc but he said that once a letter of rec is submitted, it cannot be taken back. Do you think if I talk to my science teacher he will be able to take the letter out of my app?