Audio problem: When Halloran and Hunt are discussing orders from the commissioner to exhume Jigsaw, it's clear that several of Halloran's lines have been looped in post. His voice is a bit too loud and a bit more forceful than he appears to be speaking, and at least one word doesn't quite line up with his mouth movements. It can be hard to spot the first time, but if you look for it, it's noticeable. (Confirmed in DVD/Blu-Ray commentary - the actor lost his voice and his lines had to be looped).
Audio problem: When John and another bodyguard/hitman are walking in a crowded subway/train station, and they're shooting at each other with suppressed 9mm or 45 ACP handguns across swaths of people and the people not reacting is an absurdity. High caliber handguns meaning anything larger than a .22 still makes a loud noise when suppressed. People in a general vicinity could still hear a noise and a pop. The only truly silent handgun is a .22 and it still makes a noise when the slide reciprocates back and forth. (01:18:00 - 01:18:45)