You literally just said you thought he did.
I said he probably did something to the condom, but that isn't rape, it's completely morally wrong and he shouldn't of done that. How many women have been charged with rape for ripping a condom so they get purposely pregnant? Would that be rape? If not, why not?
The act of rape though is penetrating someone with your penis without consent, he had consent for the sex, so it wasn't rape. You could argue that there should be a separate crime for not using protection but that crime shouldn't be rape, it's not the same severity and diminishes rape as a crime in general.