I still a little surprised by the 'humour' people keep mentioning in episode 3. There were a few scenes that raised a much needed smile in a very intense episode. A few scenes of Dragoon being Dragoon (not at all out of character) Arthur quite understandable serious throughout and some tender friendship moments at the end.
Having some humour and light relief during dark moments is one of the reasons why this show works for me and is the main reason why 'Camelot' did not!
Anyway, I digress.
No character on this show is truly 'black or white' that is what is so good about it. Merlin has flaws as does Arthur, which is as it should be in a book, tv show or film. There should be no place for Mary-Sue characters in a good story. Equally, the baddies are not just bad for the sake of it. We know why Uther was as he was and we know why Morgana has turned and why she thinks she's doing the right thing. As such, that Merlin/Morgana scene was about two protagonists involved in an epic battle where each try to gain the upper hand in order to achieve their goal. Morgana's constantly nervous about Emrys and his power and Merlin just wants to survive for long enought to get that jar. He may or may not have checked on Morgana once he turned young again but, as we can see from the scene straight after the fight, he could barely light a fire to burn the creature, never mind do anything else.
Yes, Morgana should have checked on Merlin and not assumed he was finished - as should Merlin - but neither of them have had much experience of fighting in that situation. Usually when one attacks they don't have to worry about their opponent fighting back. They're both young and have much learning to do (another one and a half series to be precise) . Personally, I was just delighted to see Merlin using his full magical powers for once.