Sir Francis Walsingham died in 1590, three years before the events of the film (This is presumably why various characters react to his appearance by saying they thought he was dead).
When Bill is being chased out of The Quill and the Rapier by Walsingham's men, the zipper on the back of his pants is visible.
When the Earl of Croydon is trying to hastily tidy up his house and picks up "Livelie Maidens," it's obvious that the inner pages of the magazine are empty.
When Bill enters the tavern, he makes no reaction to his possessions missing from his wooden staff.