My pup is 11 weeks and his penis has some brown spots of some sort and may look like pimples but it's peeling I don't know what to think please help

Are you referring to the skin on the outside of where his penis is (the prepuce) or penis itself (the fleshy pink part that is not normally visible)?
If on the skin it could possibly be puppy pyoderma (just a guess) which can usually be treated easily with antibiotics that you can get from your vet.
Any draining? Open sores?
Are there any other places on the body?

Yes its on the outside, there no sores or anything else

This can only be treated by your vet. Make an appointment immediately, and good luck. :)

Thank you