If you had Plague Marines in a 500 pt list and he still didn't outnumber you then there's no doubt about it, he was doing it wrong.
Anything that doesn't allow an armor save negates FNP. AP, Power Weapon, Rending...Mmm, okay... I've been doing it wrong, then.
...wait, Plague Marines only have an armour save of 3+, so shouldn't an AP3 weapon prevent their FNP as well?
(also, they have only T4(5), so an S9 shot would instant-kill them anyway)