The supposed military officer orders the use of "explosive-tipped armor-piercing rounds" for his small arms. There is no such thing for pistol and rifle caliber ammunition. The two terms are mutually exclusive.
Monica Gray is forced into the car because she has the rod. In her attempt to escape she moves the rod outside the car. All that is needed to prevent the abduction and subsequent problems is to throw the rod away.
The aliens engage in hand-to-hand fighting which involves multiple punches. These punches clearly injure each of the aliens. Bullets fired at each of the aliens do no damage, yet even without penetrating the flexible armor, they impart far more energy when they strike. Either the bullets should have done blunt force trauma to the aliens, or their punches should not have done damage.
After the RPG is fired at the cars in the junk yard, the camera briefly pans over to the person holding the launcher. For a brief moment while he's lowering the launcher, the rocket is clearly visible, still attached to the end of the tube.
(at around 1h 05 mins) After the stack of cars fall on the evil alien, on the right side of the screen (looking through the white pickup truck's windshield), you can see what appears to be the forks of a forklift, and a guy in a white shirt with long hair turning a couple times and talking. He's apparently giving orders to the forklift operator.
The goof item below may give away important plot points.
When the alien sees a helicopter hovering behind him in the distance, it is a twin-rotor transport type aircraft. His arm turns into a rocket launcher and he fires at it. When we see the impact, it has turned into an Apache-type attack helicopter.