When Matthews' friend, Michael, is watching the puppet explain his situation on TV at the beginning of the movie, the channel indicator on the television keeps changing from displaying channel 3 in one shot to being covered up with duct tape in the next.
When the SWAT team arrives at Jigsaw's lair, the clock on the wall says 7:30. After the timer in the monitor room has gone down by 90 minutes, a shot of the wall clock shows the time as 8:00 - only half an hour later.
When the SWAT team have their guns aimed at Jigsaw's heart (just after Matthews says "Hey - is this close enough?", we can see three laser guides on his chest. Then one of the SWAT team members points his gun down, but there are still three laser guides on Jigsaw's heart. Seconds later there are two lasers, then three again.
When Xavier opens the door to the Syringe Pit, it shows a very short clip showing the timer on the door for the antidote. If you slow the clip down, you will see that the timer shows '4:00', in the next scene it shows '2:58'.
The goof item below may give away important plot points.
When Gus is shot through the eye, the bullet goes through his left eye and has a pattern of blood running down his face, yet later on throughout the movie, when Xavier sees the number on the back of Gus's neck, we see Gus's eye is perfectly normal with no blood marks, or bullet wounds.