When the messenger brings Moray the news of Mary, the lighting changes markedly from the closeup to the master shot.
(at around 1h 2mins) When the document pardoning the treasonous lords is retrieved from the fireplace, it was burning to pieces. When placed on the table for Mary to sign, it was mainly intact and barely damaged despite being on fire seconds earlier.
Mary's execution takes place outdoors. It actually took place in the great hall of Fotheringay Castle.
A screen caption introduces a setting as "Holyrood Castle". Properly this building, now the monarch's official residence in Scotland, is known as the Palace of Holyroodhouse sometimes shortened to Holyroodhouse or Holyrood, but never as Holyrood Castle.
When an overzealous Bothwell pulls at the window bars of his cell, the prop bars move.
When Rizzio is stabbed, no blood is visible on the dagger, on him, or on the bed linens.
This movie about events of the 16th century concludes with a rendition of The Bonnie Banks o' Loch Lomond, a song that was not published until the 19th century.