When McGarrett is shot by the drone, he is wearing light colored pants. In the car, when he is checking the bullet wound a few moments later, the pants have changed to dark pants.
Jerry says that there is insufficient (radio) spectrum for military use, and the equipment to hijack a drone is available at any hardware store. Actually several frequency bands are officially reserved for military use, and even with the required radio transmitter, military drones use encrypted signals, so the hijacker would need to have the correct encryption keys, which of course are secret.
McGarrett, looking at a brass cartridge case, says 7.62, "military issue". 7.62 x 51mm ammunition, also known as .308 caliber, was originally developed for the M-14 battle rifle but is common and readily available on the civilian market.
When Jerry is reading off the coordinates of the operator from the drone, logically it would read off Jerry's location as he was the current operator at the time.
The drone puts many many rounds into Dannys car from behind. Many bullet holes are seen and the sound of bullets hitting metal is heard often. Despite this, not a single bullet hits the rear window. Also, the sheet metal used in cars is not bullet proof but neither passenger inside the car is hit.