Plot hole: The opaque red lined map that Otomo retrieves from his first fight is ridiculous. Why would people who know where the hidden base is be carrying around a map on them (which shows a route so basic that they'd have to be brain-dead not to be able to remember it anyway) just so that conveniently one of their enemies can get it?
Plot hole: When the elevator door sticks, he pushes the thick metal doors outward as though they were made of tinfoil. But when he reaches the room, he shoots out a silhouette in a flimsy wooden door to get in. How stupid. Total waste of ammunition and spoils the surprise factor.
Plot hole: What was the point of leaving the three men to guard the abandoned base? They would have stood no chance against any search patrol and would have simply given the Rehabs the map to the real base (on one of the three men). And why did the man even have that transparency with the red path, when he had no map to use it with? It was useless to him without a map, and only would have been a liability if he had been killed.
Plot hole: When Bertha and the gang enter the Police Ordnance depot, they find an ED-209 waiting for them. It threatens to shoot them, but instead of running, they just stand there. They didn't know the girl was some kind of computer nerd that could reprogram ED-209, but for nearly 20 seconds, they just stand there.
Plot hole: Marie and Nikko show up with a huge police van, and lots of computer equipment. Are we to believe that they stole these items from a busy police station and no-one noticed? How did they get all those heavy computers and machines loaded into the van by themselves? Did the police not notice one of their SWAT vans missing either?