My 3yr old son stands up to wee but when I sit him on for a poop he will have a wee at the same time. When I lift him off I have noticed his pants are sometimes wet at the back. They were dry before I sat him on and his penis was pointing into the toilet.
Why are his pants wet? He gets very upset because of this.
He is not fooling about because I am with him all the time.

The wee must just spray back somehow. Can't you just take his pants completely off then there shouldn't be a problem

I agree, it sounds as if some of the wee is be spraying 'under' the seat and down the front of the loo then on to his pants, try using a training seat for him it may be more comfortable and prevent these 'accidents'.

I think his penis must be pointing forwards instead of down. The wee is going under the seat and on to his pants instead of into the bowl.
Try holding it down while he wees.

I remember having wet pants or seeing a puddle on the floor after sitting on the loo for a poop. My mother used to smack me and say I was a naughty boy for having a wee at the same time as a poop. She said I should stand for a wee and sit for a poop.

Frankly, I can't see how wee can go under the seat if he is sitting on the loo correctly with his penis pointing down.
It must go down!
My sons have all sat on and their pants have always been dry after going.