I don't think it was a flag of their unit. If it was, then there should be no problem at all, as long as it's older than SS itself (which is plausible). Something like the Canadian town of Swastika, which refused to change it's name because some loon in Germany decided to make swastika his symbol. On the other hand, they don't know where did they got this flag, so it's most likely just a random piece of cloth acquired by one of the Marines who thought something like "Hey, this looks cool, let's make this our flag". Considering that it was in Afghanistan, I think it's just a honest mistake, history isn't something you think about much when in a warzone (unless you're a history buff, that is).
Also, IIRC, "SS" was a German term, an acronym (well, sort of) for Schutzstaffel.