The game has weird facing issues. Basically, from what I can tell, the server or client doesn't actually update your opponent's direction until they move. So when you open on your opponent, they turn in the instant before they get knocked down, and you move behind your opponent to backstab but cannot. This is because the check for the positional requirement is done by whichever side is not correctly updated.
It's a terrible bug, so try going at your knocked down opponent from the side. It usually works regardless of which direction they are facing and you don't have to hunt around wasting GCDs.
It's also a huge problem in pvp. If you've ever seen an operative open on someone standing on a ledge and randomly jump down while their opponent stays up, it's because on the operative's screen the knockdown threw the opponent down from the ledge. It's really terrible when you can't hit your opponent without jumping down, but as soon as the stun ends your opponent teleports back up and now you're stuck in combat for 30 seconds, can't restealth, and getting shot at from range.