Continuity mistake: Willard is setting a rat trap which has peanut butter on it, the peanut butter then disappears from the trap. It reappears again only to disappear again. (00:05:35)
Continuity mistake: When Willard feeds the rats in the basement, the container of nuts is next to a Coke bottle. When he leaves the basement, there is no bottle and the lid from the nuts container is in a different place. (00:20:05)
Continuity mistake: When the rats are tearing the newspaper, the amount of damage to it is inconsistent. At one point they've torn all the way through the blue banner at the top of the page; later it is whole again. (00:24:50)
Continuity mistake: There is a closeup of the clock at the office showing that it is 9:21 and therefore that Willard is late again. Mr. Martin shouts at him for less than a minute and then in the background you can see the clock reading about 9:35. (00:27:20 - 00:28:10)
Continuity mistake: When Willard is in his father's study he is crying. As he continues to look at his father's things, the tears appear and disappear and re-appear when he picks up Socrates and holds him to his face.
Continuity mistake: In the scene where Willard is walking to Mr. Martin's house with the rats in the bag, his hair style is different than it is in the rest of the movie.
Continuity mistake: In the scene where Willard is in his father's study, the packet containing his father's belongings is marked as being from the Brooklyn Coroner, suggesting that he lives in Brooklyn. Although, when he goes to Mr. Martin's house, he takes the 7 train (you can obviously tell, as the 7, at the time, was the only line running those old red cars). The 7 train does not run through Brooklyn at all, it runs between Queens and Manhattan.
Answer: Pure marketing. The original ending was the shot of Ben in the window, but test audiences thought the movie was too dark already. The rest of the end was filmed months later, with Willard stabbing a bean bag.