User blog comment:Aithusa07/List of Plotholes from Merlin/@comment-10341849-20130718115816/@comment-5674726-20130718152907

''But I am also think it was impossible for Aithusa to help Morgana because Morgana was not dragonlord, therefore it was impossible for her to ask or to summon Aithusa to do things for her. The worst part was Merlin WAS the dragonlord, he was able to stop Kilgharrah from attacking Camelot, he was able to ask him to help him, or to do so many things, but Merlin wasn't able to order Aithusa not to help Morgana. AND Merlin was the one who hatched Aithusa! But Aithusa didn't want to help or obey Merlin!''

Morgana might not be a Dragonlord but Aithusa had a mind of her own and, absent a command from a Dragonlord not to help Morgana, she could choose to help her. Morgana couldn't command but she could and did ask, and Aithusa chose to help her when she could.

Just because Merlin is a Dragonlord, it doesn't mean that all dragons were going to feel any loyalty or affection towards him. Maybe Kilgharrah did, or maybe he just thought it prudent to let the man who had the power to command him to stand still and not resist while he was slaughtered believe that he was on his side, whatever his true feelings. I know that the guy robbing me of my free will would be the last person I would feel the slightest hint of true loyalty towards. I certainly don't blame Aithusa for wanting nothing to do with him.