It seems while I was fighting the Hydra, I first used an Assassin Strike on the Ebon head, bring the head back under, causing me to take down the 3 heads first to bring him up. When he goes underwater, that means he cannot attack me at all until he is up again, right?
Well, that wasn't the case for me.
The Cobalt head was the last head to take down before the Ebon head would rise again. When I moved my El Toro up to attack the Cobalt, I saw the name, Ebon, attacking my El Toro. The problem is that the Ebon head never rose up because I did not take down the last head. So my Toro was getting hit by an invisible Ebon head who, unfortunately, landed 2 Mega Hits on El Toro and immediately took him down.