Plot hole: In 'The Foretelling', it is said that Richard IV reigned for "13 glorious years" with a caption showing 1485-1498. 'The Black Seal' starts on St. Junipers' Day, 1498, but Blackadder spends 12 months locked up with Mad Gerald. So when the Royal Family are finally murdered it is actually 1499.
Visible crew/equipment: In the final shot where Percy and Baldrick have entered the room and said their lines, as it fades to black the crew can be heared applauding.
Revealing mistake: At the very end of the episode, right after Edmund drinks the wine, the camera switches to a close-up. Watch the very animated 'dead' extra right behind Edmund who seems to be unsure whether the scene is in the bag yet or not. (00:29:25)
Character mistake: After firing Percy and Baldrick, Edmund says to Baldrick that he'll probably go back to shovelling dung in the gutter where Edmund found him. In the pilot episode The Foretelling, Edmund actually met Baldrick when Baldrick was pouring a drink for Edmund.
