Let me get this straight.
- Your son went to a car dealer
- Your son negotiated a price
- Everybody signed paperwork
- Your son then went to the bank with the paperwork and got a cashiers check.
- Your son delivered the check to the dealership
- Everybody signed more paperwork
- Your son drove away with the car
- Now two days later they want more money.
I would stand my ground. Your son negotiated in good faith. Either they messed up, or they are dishonest. Either way your son wasn't the one supposed to know all the internal rules.
I don't think it matters if they cashed the check or not. I would tell them if they have cashed it, that is even more evidence the deal was finalized. But even if they they didn't cash it, it only proves they are very disorganized.
If for some reason your son feels forced to redo the deal, have him start the negotiations way below the price that was agreed to. If the deal for some strange reason gets voided don't let him agree to some sort of restocking fee.