(at around 7 mins) When Peter Strahm is walking through the building with his gun raised, and he is checking all of the corners in the building, he holds the flashlight on the wrong side. Police are trained to hold the flashlight on the opposite side of the gun, with the left hand going under the right hand. So, for example, if you are right-handed, the flashlight, held in the left hand, goes on the right side.
(at around 6 mins) In the part where Agent Strahm is in the room where Jigsaw was killed, when he (Strahm) unveils his phone, he tries to phone someone. When it says 'NO SIGNAL FOUND' if you look carefully at the top-left hand corner, it shows very high signal level. Also if you look at the bottom of the screen you can see that Strahm actually uses blue-tooth for which it is shown that 'NO SIGNAL FOUND'.
In the film, Erickson is constantly wearing a BlueTooth headset. When Hoffman calls him from Strahm's mobile phone, he answers the phone as normal, not using the headset. He appears to repeat this when he tries to track Strahm's mobile phone.
During the pendulum trap scene: When we see Seth's face for the first time, the collar around his neck appears to have a bolt in the center on the underside holding it closed; however, once Seth dies the collar opens and we see the bolt is missing.
In the scene where Jigsaw is talking to tied up Hoffman, when Jigsaw shows him the newspaper, before he says "especially inferior work", in the close-up, you can see Jigsaw's mouth moving when no noise is coming from it.
In the room with the mounted razor traps, a timer on the wall is shown to begin counting down from 15:00. However, a few seconds later Charles points to the timer, and it is shown with 15:00 on its display again. The beeping heard once the timer has begun also stops in the next few shots.
Maybe it's just the splicing in of extra footage into the director's cut, but when the first victim is getting sliced in half, it slices his body almost completely in half and then shortly after repeats the shot where his stomach is getting one of the first slices.
(at around 8 mins) If the extremely speeded-up shots during the cube scene are examined frame-by-frame, there are several single-frame cuts in which crewmembers can be seen working around the cube. One in particular shows Scott Patterson with a relaxed expression, with a face towel inside the cube and the cube lid partially open. Two crewmembers are working behind the cube and the hand of a third can also be seen.
When Jigsaw is talking to the detective at one point he opens the shotgun and we see a cartridge in the left barrel. Moments earlier when the detective is tied to the chair, jigsaw pulls the front trigger and it is blank. Traditional double-barreled shotguns have the left barrel connected to the front trigger and the right barrel connected to the back trigger so when Jigsaw pulls the front trigger it should shoot, since there is a cartridge in the left barrel.
In the bathtub trap room, the three surviving characters are told that they have three minutes to "bridge the gap" and unlock the door to the next room. A timer above the door shows 15 minutes, but this one is connected to bombs in the corners of the room (something not mentioned on the videotape); the three-minute timer is set up separately.
The tank around Agent Strahm's head did not necessarily need to be airtight. It was secured in an upright position by two metal bars attached to the ceiling, and could therefore have had an air hole in the top panel that would not have prevented death by drowning.
When John Kramer and Mark Hoffman are seen setting up the house used in Saw II, they clearly have no gloves on and therefore are leaving fingerprints over everything they are touching. This would clearly reveal at least Hoffman as an accessory to these crimes and he would have been identified very soon afterward. However they could not have been found out for the house was never found in any of the movies
(at around 1h 7 mins) Hoffman steals Agent Strahm's cellphone out of the evidence locker, and uses it to call Erikson. Erikson answers the phone thinking it was actually Agent Strahm. However Erikson should have known that Strahm's phone was in evidence, and therefore known that it could have been someone else using the phone.
When John Kramer and Mark Hoffman are seen setting up the house used in Saw II, they clearly have no gloves on and therefore are leaving fingerprints over everything they are touching. This would clearly reveal at least Hoffman as an accessory to these crimes and he would have been identified very soon afterward.
(at around 11 mins) The old lady in the waiting room is reading a magazine with an article entitled "The Two Faces of Jigsaw". Only the first paragraph of the article is about Jigsaw, the rest is repeating text about parish houses.
(at around 29 mins) The first three newspaper articles that Strahm looks up on the computer about Seth Baxter all contain the same exact text, even though they're about three different (albeit related) subjects and were written by two different authors.
(at around 36 mins) When Charles takes over breaking the hanging jars in the second room that the remaining four of the fatal five encounter, at one point you can see some of the rubber glass bouncing on the ground.
(at around 40 mins) In the elevator scene where Hoffman is attacked by Jigsaw, Hoffman enters the elevator on ground floor and selects 9th floor. You can hear the elevator ringing a bell for each next floor it reaches on the way up, however the elevator does not stop at the 9th floor.
The goof item below may give away important plot points.
Incorrectly regarded as goofs
At the end, when Brit and Mallick are in the room with the saw machine, Brit realizes that all five captives could have survived to this point by working together in the previous three rooms. Billy's "odd man out" comment seems to contradict this idea, since the second room had only three bomb shelters that could be unlocked. However, it is stated that each shelter could have held two people; the "odd man out" would have been the person in a shelter by himself/herself. Further, there was the conversation about being able to predict human behavior. Hoffman predicted they would assume one person would die in each trap.