Continuity mistake: All the castle windows on the outside of the castle are small squares yet from inside the rooms they're arched.
Other mistake: We see the letter about Merlin being written with a quill. However, despite the length of the letter being written we never see the quill being re-inked. (00:08:20)
Continuity mistake: During the Treaty signing Merlin's cape collar goes up and down depending on the type of shot it is - close up the collar is up, distance the collar is down.
Continuity mistake: After Merlin drinks from the goblet he puts his empty right hand up to his face. However, when he collapses the goblet is shown falling out of his right hand.
A Remedy To Cure All Ills - S1-E6
Character mistake: King Uther calls the Lady Morgana, Morgause. (00:11:50)
Factual error: Merlin says they threw potatoes at him. Potatoes were only in Europe from the 16th century on.
Other mistake: When Uther takes Excaliber from Merlin while preparing for his duel with the black knight, we see that Uther is left handed. And he is left handed while writing. He tests the balance of the sword with his left hand, and in fact wears his sword on his right hip in all other episodes. Once he puts his helmet on and begins his duel with the black knight he suddenly becomes right handed.