Mudguards can get misaligned quite easily. I have had that happen quite a few times on different fenders at different times. Nothing to do with the frame at al. Not sure why you would scrap a frame because your fender is misaligned but I am guessing you have loads of money and if so share some with us. I would love to have enough money to throw away a bike, I wouldn't do it but it would be nice to have that kind of cash.

If your dropouts are damaged post pictures so we can see what is going on and make suggestions but otherwise just adjust your fenders or have a shop do it. Not uncommon.