Multiple duplicate keys from many shops

I'd be surprised if Fanatical was selling dupes (it happens, but it's rare, and they're really good to deal with generally).
I assume you've made sure the other guy is trustworthy?

you can always ask Steam as to when those keys were redeemed

Usually these revocations get tagged on Barter. Yes, I've had many different keys from various bundles that don't work even when I've just revealed them for the first time and immediately try them on my account.

If it happens across multiple sites, it's almost always an issue with the developer/publisher behind the game (which in turn makes it unclear whether or not you'll be able to get a working key, as well as making it clear to the storefronts in question that there's a widespread issue). At that point it's best to ask for a refund [which most storefronts will usually give as store credit]. I hear Lootboy offers replacement games, as well, so you may be able to get it sorted at every front.