As I recall, you still haven't played Mass Effect 3. There was a bit of dialog that addressed that. Liara is talking to Javik (the Prothean squad mate from the day 1 DLC)about how they were the only race active in their cycle. He corrects her and says that there were other races that had been conquered and subsumed into the Prothean Empire but eventually "all called themselves Prothean" or something to that effect. It doesn't really mean much in the grand scheme of things, but it explains the existence of the Prothean Cypher that Shepard got from the Thorian in the first game.
-------- Wedge Defense Force General Order 12: "Try to avoid freaking the mundanes."