As Elizabeth is being arrested, Robert Dudley's gold chain suddenly disappears from around his neck.
Elizabeth has flashbacks to the Bishop shouting "You'll be damned for this!". But the Bishop shouted this at Walsingham, not Elizabeth.
After the unsuccessful assassination attempt, when Elizabeth is being tended by her ladies, she is shown standing, yet the very next shot has her sitting.
As Walsingham is speaking with Mary of Guise, she is holding a table knife up to her lips, and is playing with it by rotating the handle. The camera then switches to a shot from behind her head and the knife is oriented the other direction. Then, as they continue speaking, the camera shot returns to the original angle and the knife handle is reoriented back to the original hand.
In the scene when Robert Dudley goes to Elizabeth's bedroom, he interacts with six 'ladies in waiting' who are giggling outside the room's entrance. He flirts with Kelly MacDonald's character and then goes inside the room. In the next shot, Lily Allen's character suddenly appears and there are now seven 'ladies in waiting', positioned differently in the entrance when Sir William Cecil interacts with them immediately after Dudley enters the room.
At the beginning of the film when Elizabeth is being arrested, she is addressed as "Princess Elizabeth". She was stripped of the title 'Princess' when Anne Boleyn was executed and called 'lady'. Mary Tudor made certain that distinction was maintained during her reign as she followed Catholic Law and considered Elizabeth a bastard.
The beginning of the film shows Robert Dudley with Elizabeth while she was arrested. Historically, Robert Dudley, his four surviving brothers (including Guildford), and his sister-in-law (Lady Jane Grey) were all in the Tower of London indefinitely. In fact, Wyatt's rebellion threatened all of their lives and brought about the executions of Jane and Guilford, while Robert and his remaining three brothers would stay in the tower until being released later that year.
While it's true that Henri, Duke of Anjou (later King Henri III) was generally obsessed with clothing and did on occasion dress as a woman, he never actually traveled to England to court the Queen. That honour fell instead to his younger brother François, who became Duke of Anjou in 1576, and was the only one of Elizabeth's many suitors to court her in person.
Walsingham never went to Scotland during the period the film covers and never killed Mary de Guise. She died of dropsy. In fact Walsingham later went to Scotland to ensure James VI's succession of Elizabeth to the English throne. Walsingham is also portrayed as older than Elizabeth in the movie, but they were about the same age.
The movie shows Kat Ashley as being about the same age as Elizabeth when in actuality she was much older than Elizabeth was.
At opening scene on the right side of the shot, a halberd used to block the crowd from the prisoners bends and wobbles, showing itself to be made of rubber.
When Elizabeth, dressed in red, is galloping to find Sir Robert, who is afield hunting, one long shot taken straight on shows the face of the stunt double.
The first shot of Walsingham in the film (from behind the head), is actually used twice. Just before the next shot (of his face), a sharp slit of silver can be seen heading toward Walsingham's head from the right side of the screen. However, Walsingham's servant then crosses the room, and gets a knife out of its case. When the next shot of the back of Walsingham's head is seen, this slit is the knife now being held to his throat by the servant.
When Walsingham enters the Arundel home looking for the priest he picks up the little girl and if you look closely you can tell that he's holding a doll.
Robert Dudley recites Sir Philip Sidney's sonnet "My true love hath my heart" to Elizabeth in a boat. This sonnet was not written until at least 1580, about 20 years after the time the movie is set, and wasn't published until 1593.
Elizabeth is shown washing her face with water. In 16th-century England, water was considered dangerously unhealthy and almost never used for washing the body. Elizabeth would have "bathed" by rubbing her face with a dry cloth.
Thomas Howard, 4th Duke of Norfolk was not arrested and executed for treason until 1572 when Elizabeth was 39, and well outside the time period of the movie.
In the film, Bishop Stephen Gardiner stands as a key figure in the pro-Catholic faction during Elizabeth's reign. In fact, he died in 1555 before Elizabeth ever ascended to the throne. The role Gardiner plays in religious politics here is likely a stand-in for the historical Bishop Edmund Bonner, the Catholic clergyman most at odds with Elizabeth's Protestant reforms, who died as her prisoner in the Tower of London in 1569.
Mary of Guise is seen wearing modern eyeliner and eye shadow throughout the film. It's especially conspicuous when she is having dinner with Walsingham during his visit to Scotland.
At 1:23:12, midway up the Scottish castle in the background, the flash of a passing car is visible.
John Gardner refutes Elizabeth's description of religion as a "small" issue by saying that it led to her mother's death. Elizabeth's mother, Anne Boleyn, was executed for adultery, not for her religion.