Just put a onesie under the outfits. That's how every baby I've ever seen wears clothes like that. They are meant to be worn alone.
Wait...strike that. You have a 3 MONTH baby in 9-12 months clothes!! Good grief! I'm surprised anything fits:-) Just tell the grandparents that the clothes don't fit. When they are given to you, take them, say thanks, then casually ask for the receipts, "in case they don't fit." Add, "he's such an unusual size for a three month old that we have had a hard time finding clothes that fit. The last few times he hasn't been able to wear them."
If they refuse to listen, just set the clothes aside and either save them for later (maybe he will thin out and the clothes will fit later), sell them, or give them as gifts (since they will still have tags.)