Plot hole: Even if the 30 bus passengers that were already dead had been burned up in the explosion of the building their bodies would still have been autopsied after the fact, thus proving that Phoenix had killed them beforehand and vindicated Spartan.
Plot hole: When Spartan jumps through the window in the excavation scene of the museum, he crashes into a room with bottles of drink on the shelves. Surely this room too would have been filled in and the window smashed during the earthquake, and the museum wouldn't have bothered to excavate it as it can't be seen from above due to the blanked out window. So what is that room doing there? (00:49:20)