During the autopsy of Capt. Hallard, the police LT reports to the Deputy Director that Hallard had his hands secured behind his back with his own cuffs when he was shot. Yet in the previous scene, when the bad guys are covering his body in the dumpster with a plastic sheet, his arms are straight at his sides in the dumpster.
During the autopsy on Capt. Hallard's body the police Lt. is describing how Hallard was shot 3 times in the back, while the ME is removing a bullet from the body. The only problems are a) Capt. Hallard was shot in the lower left quadrant of the back but the ME is digging around in the area of his left shoulder, b) there is no "Y" incision which would have been made in order to examine internal organs and facilitate removal of the bullets, c) the autopsy is being performed while the body is still in a body bag.
During the gunfight on the roof of the parking garage, you can see the squib flash when the big guy in the white shirt gets shot. The squib actually goes off AFTER he has already started to react to getting shot. Also, as he hits the ground you can see the cable used to trigger the squib coming out of his left pant leg.