Great movie, but a few glaring issues

Rating: 8/10 (19 May 2013)

Saw the movie today, and I was right into it until the final fight near earth then things seemed to go from great to "WTF".
So just 265k km from Earth by the moon an unregistered starship and the Enterprise are going at it, and the Earth perimeter defence picks it up and then they... what? Go for coffee? Are away from their posts? Are ordered to ignore it? Or can any ship warp in by the moon and it's the great Earth blind spot? Then the Enterprise "suddenly" is picked up by Earths orbit and starts spiralling in. And what does Starfeet do? They couldn't pick up 2 starships by the moon, so now that they are in Earths orbit I'm thinking they maybe noticed by now. "Should we beam them out Sir? The Starship is spiralling in out of control and we're Federation HQ and have lots of transporters". "Nah, let them handle their own problems, they have Kirk and Spock they will figure it out in an overly dramatic way".
Then the big dark starship flies at high speed into San Francisco and ... lands like it's going 60 kph. Sure, it wouldn't go up like a thousand nukes when it smacked into the planet like a giant meteor coming in.
Then these guys are jumping on ships. Clang. No one notices and just keeps flying like this is like hobo's hopping trains.
Great movie, last 15 minutes were very poorly constructed.