When Ben stands up after retrieving the button from the trash can in Katherine Randolph's office, he is obviously wearing knee pads under his pants.
At the trial Ben explains that the victim was looking at the digital counter upside down, reading the numerals '337' as the letters 'LEE', to explain the clue that he left. However, the victim was laying on his stomach when he reached up to stop the tape counter, which means he could not have been upside down.
Dan was holding a lit cigarette when he was killed and fell to the floor, but the cigarette somehow ended up positioned perfectly in the ashtray on the stand above him right afterward as if someone had intentionally put it there.