Kate says that the victims were shot "with tight grouping, three shots each." The victim in the passenger seat was shot four times in the opening scene.
After McGee tells Kate that the corn snake Tony is holding is not poisonous, Kate kicks Tony. When Tony falls down, the snake has disappeared.
At 09:47- the two officers are oblivious to the fact that they just heard a loud explosion.
Right after Gibbs shoots the terrorist piloting the drone and approaches the controls, the joystick is shown leaning all the way forwards, which would crash the drone. Gibbs and DiNozzo are both seen to approach the control box, and the joystick is upright again.
To cause the drone to crash Gibbs shoots the control unit. As no one had been actively controlling the drone, and the fact it was homing in on a beacon, it would most likely be flying on an internal autopilot. Shooting the control unit would not change anything in the drone's flight and it would continue its mission as programmed.
The correct course of action would have been a forward push on the joystick. This would override the autopilot and cause the drone to nosedive into the water.
McGee and Kate keep referring to a snake as poisonous. Other than constrictors, most land snakes are venomous not poisonous. They attack injecting venom through their fangs. Some snakes are poisonous, but only when eaten and the poison in their flesh is ingested in the same manner as poisonous mushrooms.
The two bullet holes that appear in the side of the car when McGee is shot at by the terrorist in the window appear straight in, instead of at an angle. The next shot shows McGee returning fire almost straight over the car and at an upward angle.
Gibbs says that the victim lived in Georgetown, which is an old, urban, upscale, expensive, densely populated area in Washington, DC. First, it's highly unlikely that a young petty officer would live in Georgetown or could afford to do so. Second, the fictional home in question is a modern, contemporary single-family ranch house with a five-digit number and a grassy lawn in a woodsy neighborhood with a curved street with little vehicular traffic and few pedestrians.
You can see one of the corpses blink when Kate has the snake wrapped around her leg.
When being helped back to her feet after she was hit in the vest, Kate says that she was shot at "point blank range". A former secret service agent would not make such a mistake; she was shot from several metres away, no where near point blank.