After the boys exchange roles, as the Prince (dressed as Tom) goes out to get his dog at the stable, he picks up a large candle, but when he comes out the door he no longer has it (at 0:32:36).
Henry VIII's death scene seated in the throne room is invented, as he actually died in bed on 28 January 1547.
The coat of arms that appears at the title sequence shows two dragons holding the shield. It should instead be the lion of England at the dexter side (at the right side of the person carrying it) and the Dragon of Wales at the sinister (the left side of the person carrying it), the coat of arms used by Henry VIII (who reigned from 1509 to 1547) in the latter part of his reign.
The right figure on the coat of arms is a stylized lion and not a dragon. The dragon on the left clearly has wings, scales , clawed feet and an arrow headed tale. The figure on the right has none of these. The same coat of arms is much clearer above the boy king's bed around the 1:02 mark where the dragon and lion details are not obscured.
(at around 1h 45 mins) Lord St. John rushes to Edward's room to retrieve the Great Seal. As he leaves the room without the Great Seal, the door is left partially open; in the next shot of two guards standing at a door, the door is closed. As he comes out, the lines in the floor design run parallel to the length of the hall, but the door to Edward's chamber is at a 45 degree angle with the floor lines. In what appears to be a reaction insert shot where the door is closed, the door is parallel to the floor lines, which means this is a different door, further down the hallway along which Lord St. John runs past numerous posted guards.
(at around 8 mins) While with Tom Canty, Father Andrew is seen wearing modern spectacles. This was not possible in 1547 as the modern style of spectacles, held by temples passing over the ears, was developed some time before 1727, possibly by the British optician Edward Scarlett.
It is easy to tell the difference between the twins, especially as Robert J. Mauch has a larger chin than Billy Mauch.