(at around 1h 17 mins) After Jeff and Halden get out of the vat of puréed pig they are dry and clean for the rest of the film.
In Saw II (2005), Amanda Young slit her wrists with razor blades. In this film the cuts would have healed but left marks or scars. There are no visible marks or scars on her wrists but in Saw VI (2009), the flashback sequence which took place during the events of this film clearly make a reference to the scars on her wrists.
(at around 1h 11 mins) In Saw (2004), Cary Elwes's character Dr. Lawrence Gordon is blonde. However, in the bathroom preparation scene in this film, Elwes's stand-in has very dark hair.
(at around 1h 2 mins) When Lynn is operating on John's head, she cuts the skin from the skull and then clips off some veins. Right when she asks Amanda to fill the syringe with alcohol to clean John's head, Lynn turns back to wipe up some of the blood, but there are no clips in place. A shot after that, she is seen taking the syringe from Amanda's hand and squirting the alcohol on John's head and the clips are there.
(at around 49 mins) The picture Jigsaw shows of Amanda in the flashback before she is captured and placed in her trap is actually a photo of her from Saw (2004), where she is interrogated about Jigsaw and explains what happened to her after she was in the trap.
(at around 9 mins) The Achilles tendon needs to be attached to both the calf and the heel in order for the structural integrity of the leg to work: detach it from either end, and the foot is structurally unable to bear weight. When Troy tears the ankle chains through, he destroys the link to his heel, and he would fall over.
(at around 1h 21 mins) Though certainly capable of inflicting horrendous agony upon its occupant, "The Rack" trap would not splinter Timothy's arm and leg bones as shown in the film. The continuous twisting motions would dislocate the bones from each other and possibly cause them to penetrate the surrounding skin, but they'd otherwise remain in one piece. It is also likely that under so much pain, Timothy would have blacked out into a coma before the trap sequence concluded.
(at around 18 mins) When Lynn treats the child's pneumothorax with a drainage, the nurse exclaims that the patient is improving. However, at that moment the monitor shows a ventricular fibrillation (VF), a severe arrhythmia that causes death unless immediately treated. Moreover, the VF spontaneously turns into a stable "normal-beat" heart rhythm without an electrical shock, situation that's almost impossible to see in the clinical practice.
(at around 41 mins) In the "Freezer Trap", Jeff shivers while the naked, prone, watered-down Danica doesn't.
(at around 36 mins) Lynn tells Amanda that John needs steroids like prednisone to help relieve his brain swelling. Amanda replies by saying "or maybe instead we should try some corticosteroids like dexamethasone, tell me something I don't fucking know already". Prednisone is a type of corticosteroid and is very similar to dexamethasone, although dexamethasone is better suited to relieve intracranial swelling than prednisone.
(at around 36 mins) Lynn tells Amanda that they need to take John to a hospital because drugs like prednisone and dexamethasone can only be given in a hospital. Corticosteroids like these are prescribed to be self administered all the time, especially prednisone which is the most commonly prescribed corticosteroid to relieve pain and swelling caused by arthritis, or to help relieve the itching and swelling from rashes and a number of other conditions that cause inflammation.
(at around 57 mins) When Jeff tells Halden "you only gave him six months" (meaning Timothy Young only got six months for killing Dylan), Halden says he can give him more time. "There are ways." Due to Double Jeopardy you can not be tried for the same crime twice. Timothy was tried convicted and sentenced already so there is no way he would get anymore time.
(at around 14 mins) In the "Angel Trap" Detective Kerry is told she has to reach in and get the key out of the acid. Right after the tape finished playing, we see her struggle with the chains holding the beaker for a second and then reach into it. This shows us that because of the way the beaker is suspended and the way she is restrained, she is unable to tip the beaker far enough to spill any of the acid.
When Lynn is wearing the "Shotgun Collar", close-up/insert shots show the primers on the shotgun shells already discharged. This means the shells had already been fired and would not work. While it could be imagined that empty shells were used as containers for explosives, this is inconsistent with the collar's design (hammers are set to strike each cartridge) and effect (the collar, cartridges, and most of the victim above the chin are intact after firing).
(at around 1h 29 mins) Shawnee Smith is seen biting down on blood capsules while she is being bashed into a wall by Donnie Wahlberg.
(at around 40 mins) When Jigsaw pulls out the tape player, his thumb is on top of the tape player, nowhere near the play button on the side of it. However, a click is heard, as if the play button had just been pressed, and the tape begins to play, even though the play button was never pressed.
(at around 10 mins) On the right leg after the explosion in the classroom, the torn Achilles tendon is not seen, although it was torn from the knocker of a chain.
(at around 1h 17 mins) Just as Jeff and Halden walk out of the "Pig Vat" room, they walk through some plastic. When Halden walks through it the camera is reflected on his back.
(at around 45 mins) When Jeff's cheek is stuck to the pipe, a cameraman's shadow on his shirt is seen.
(at around 38 mins) A boom arm is seen when Lynn is asking Amanda for Ativan.
When Lynn Denlon's surgery on John Kramer appears, a very quick reveal of a pair of fingers tossing fake blood onto her face appears from the left side of the frame. While it is not shown in the movie it is shown in the montage at the end of Saw 3d.
(at around 42 mins) If Danica was the only witness to Dylan's death and never reported what she saw, how did anyone ID Timothy as the hit-and-run driver in the first place? Furthermore, Danica's role as a witness would also remain a secret. Assuming Jeff saw her, they were still complete strangers, and he'd have no way of identifying or contacting her. Seeing her would also make Jeff a second witness, negating Danica's "only witness" role completely.
(at around 6 mins) The rings in Troy's flesh appear to be solid, singular objects with no visible seams or hinge mechanisms, and thus no viable way to be opened and stuck into his skin as depicted.