Now, there's been plenty of speculation as to the origins of the Qunari already, so it's possible I won't be adding much to it, but something about them bother me. Some brought forth the theory that they were created by Ghilan'nain. possibly, but then, why is it that Corypheus would know enough about them to call out to an Adaar Inquisitor "The Qunari are not a race, they're a mistake". As far as we know, Corypheus has no special knowledge of old elvhenan. What he knows is what his people knew at the time he was alive. He's not a telepath and he's not omniscient. After all, he doesn't recognize Solas for even an ancient elvhen, much less the Dread Wolf.
Now, going back to the wiki article on the Qunari, I saw this : The Kossith, ancestors to the Qunari before the Qun was a thing were for the first time seen in Thedas when they had a small enclave in the Korcari Wild around -410 Ancient (and were not seen again for a thousand years after that). According to the chant, the Magister would have entered the Black City in -395 Ancient, which is also the year the first Blight started. Accordingly, Corypheus woul have been alive in -410 Ancient, but how would he know of one small enclave so far south of Tevinter and in the Wilds? I admit, it's not completely impossible he would know, but would he truly know enough about them to then call Adaar "a mistake"?
Here comes my theory (fun!). What if the Qunari (or Kossith as they were originally called) are an even younger race than we've been led to believe? If not the old elvhen, who could have created a race? Well, the Tevinter might have had had both the knowledge and the power. Around -410 Ancient, it's far from impossible that the 7 magisters, priests of the Old god, had already started planning how to enter the Fade. Now, elves make the best sacrifices, but what it they'd tried to come up with something even better, by... let's say, combining elvish blood to dragon blood, which we already know is quite potent. But, the result didn't please them for some reason. The new race was powerful, hard to control and didn't actually make for better sacrifice. Perhaps some of them even escaped their captors (that enclave in the Korcari wild). Perhaps some even manage to flee further, across the sea, or they were banished there when they became too hard to control (although I lean toward fleeing since I don't see why the magisters wouldn't simply kill their mistakes instead of banishing them). That would explain why Corypheus know so much about a race he would never have met before (and might never have heard about before, even if he somehow got it mentioned to him that Kossith had appeared in the Korcari wilds. Why make the link between those and the current Qunari, unless he somehow knows more?)
This would also explains the Qunari's fear and distrust of mages, even if most don't remember the reasons anymore. Having been created specifically to be blood sacrifices would make you wary of magic, that's for sure.
Now, if the Kossith/Qunari are a tevene "invention" I'm left with the question : Who are the scaled ones mentionned in the Deep Roads? And who are the dragonny-looking creatures depicted in elvhen murals? Could they be the same. Another race we know nothing about. Or perhaps extinct. Or perhaps I'm overthinking Corypheus' comment.