When Boze's interview starts, his neck is bare. When Mandy asks "How does it feel to stick the landing?", a scarf appears around his neck. It disappears in the next shot when Boze says, "There are worse things.:" then reappears when he goes over to talk to Mac.
The missile is supposed to be GPS-guided.
GPS requires radio signal input from the GPS satellites, and would not work inside the pipeline.
When they arrive at the water plant they arrive at a sewage treatment plant not a water pump station. Most sewage treatment plants are not in the centers of cities due to associated odors.