When Elizabeth visits Mary Queen of Scots, Mary is wearing a large crucifix and chain. A few moments later, Mary's crucifix has vanished from her chain. When Elizabeth leaves, the long shot shows the crucifix has returned.
When Leicester says to Elizabeth 'Kiss me, Bess' his hand is placed on the back of her neck. When the camera changes angle his hand has moved to her cheek.
The poem Essex is supposed to have written to Elizabeth on the day of his execution was written by Chidiock (Charles) Tichbourne (1558-1586) just before his execution for his part in the Babington plot, a conspiracy to assassinate Elizabeth.
Although Elizabeth is portrayed as travelling incognito to meet Mary Stuart (Queen of Scots), the two famously never met. They did communicate by letter and Elizabeth often expressed her wish to meet Mary but she always insisted that would only happen once Mary had acknowledged Elizabeth's right to the throne of England.
During the execution of Mary, Queen of Scots; as Elizabeth's envoy is speaking how best to inform the Queen of the beheading; they are outside, in a courtyard. Contemporary accounts show that Mary's real execution took place indoors at Fotheringhay Castle.
When Elizabeth quotes Shakespeare's Sonnet 116, "Love is not love which alters when it alteration finds", she's quoting a sonnet that wasn't published until 1609, 6 years after her death.
In 1579, when the series begins, Queen Elizabeth was only about 46 years old. By contrast, Hellen Mirren was 60 at the time of filming. This makes suspension of disbelief very difficult when the doctor assesses that she is still of child-bearing age. Hellen Mirren does not become age-appropriate to play Elizabeth until late in the series.
Elizabeth uses a fork when having dinner with Leicester before the battle against Spain but the fork was not introduced to England until the early 17th century when James I was on the throne.
While waiting on the beach to see if the Spanish Armada was about to invade England in 1588, Robert Dudley, first Earl of Leicester, pulled out his telescope to check the flag on a ship that was sailing up the river. The Telescope was invented by Hans Lippershey in 1608.