Continuity mistake: The two vials are identified as Valerian sleeping potion (clear liquid) and Henbane (yellow liquid, deadly poison). Gwen pours the yellow liquid in the king's cup, but it's supposed to be the Valerian potion used here that puts the king to sleep. Gwen later dumps the sleeping potion into his ear when it should have been the poison. Then at the end when the Merchant identifies the 2 vials he identifies the yellow as Valerian and the clear vial as Henbane. (00:18:35 - 00:24:25)
Factual error: In the show Gaius wears glasses, except eyeglasses first came into use in the late 13th century while the legend of King Arthur is around the 5th or 6th century.
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.
The Tears of Uther Pendragon: Part Two - S3-E2
Visible crew/equipment: When Morgana is hiding from Gaius there is a mic peeking out of the corner of the bed in the lower left corner.
The Darkest Hour: Part Two - S4-E2
Revealing mistake: At the very beginning of the episode, as the knights are about to send Merlin to Camelot with Lancelot, the knights walk towards the camera. As they do, there's a patch of green screen the special effects department must have forgotten to remove between Sir Elyan and Sir Percival. (00:02:10)
Visible crew/equipment: When Arthur goes to Dragoon to ask for help, when Dragoon runs out of the hut to turn back into Merlin, on the left hand side of the screen you can see a camera crew in modern clothes. [Fixed in Netflix version]. (00:23:00)
Suggested correction: I don't see any crew. I'm watching it on Netflix. Perhaps they fixed or perhaps they edited it out after realizing the mistake. But they aren't there anymore.
Even if Netflix corrected the mistake doesn't mean the mistake is now invalid if the mistake existed in the original BBC One airing. Netflix is known to change or edit programs they stream (such as replacing soundtrack songs).