These might have been addressed before, but I don't have time to look them up on the forums. Anyway, these deal with Star Trek 4 and First Contact.
In First Contact, after the Phoniex reaches orbit and seperates from the first stage, it keeps going up. Unless they activated impulse drive or something, they wouldn't have the momentum to keep in orbit for long, not to mention LEAVING orbit!
In ST:4, the bird-of-prey warps out of the atmosphere. I'm sure even with "aerodynamic shields" of some kind, that that would make a fairly loud sonic boom! Just a boom from an F-14 going 800 mph is considerable (belive me, I experinced it first hand.)
And here's a miscellanous bit. The ship seen in Alameda isn't the real Enterprise. That's the USS Ranger, an Independence class carrier now decommisioned. The real USS Enterprise has a distinct island design (that's the tall thing on the flight deck.) The Enterprise's island is more or less cube shaped, with a smaller "neck" attaching it to the flight deck. Belive me, I know. I work there!
And their you have it!