Mary did not raise her niece Elizabeth as is implied. Elizabeth was royalty and had her own household. Primarily, she was cared for by Margaret Bryon until she was four, at which point Kat Ashley took over her upbringing and education.
At the end of the film, after Mary goes to her mother to take Elizabeth, she switches from carrying the child laying in her arms in the shots from the front to carrying her on her hip in the shots from behind.
Written at the very end of the credits is the message: "This is a work of fiction. The characters, incidents, and locations portrayed and the names herein are fictitious, and any similarity to or identification with the location, name, character or history of any person, product or entity is entirely coincidental and unintentional." However the novel and film are based on the true stories of Anne Boleyn and Henry VIII with real people, historical events and locations that are also factual.
Although Mary is referred to in the film as the younger sister, most historians today are convinced that she was the eldest girl. Her date of birth is circa 1499, while Anne is believed to have been born in the early 1500s (historians continually debate between 1501 and 1507). The book that the film is based on was written with Mary as the younger sister, so the film itself makes no mistake in this arrangement.
The goof items below may give away important plot points.
Anne's pearl choker with the B on it has a clasp while she is praying and Henry comes and sits behind her. When she is about to be beheaded she is shown taking off the same choker but now it is tied with a ribbon instead of having a clasp.
When Anne's second pregnancy miscarries, she orders Mary and George to get rid of the dead fetus. During her line, "On the fire with it", you can see Mary stand up behind her. In the very next shot, Mary is still on the ground and just starting to stand up.
George Boleyn is shown being dragged crying to his execution, where the crowd is booing. Actually, George Boleyn died with dignity, after saying a long speech, which was recorded in full, meaning the crowd must have been fairly quiet.
In the end, Mary lives happily ever after with William Stafford. No one explains what happened to William Carey, who she married at the beginning of the film, but he actually died of the sweating sickness. The DVD version includes Carey's illness and death in the deleted scenes.