Trivia: I was reading through some of the entries concerning the Borg in the Star Trek Encyclopedia, and came upon a comment they had about Wolf 359 - it's the name of an actual star in space, it makes up part of the Constellation Leo. It's also the site of the first major fleet battle between StarFleet and the Borg. Take your mind back to the scene where Zef and Lily first walk out of that bar, and Lily sees a speck of light that is actually the Borg Sphere, and asks Zef what it is. He replies "That, my dear, is the Constellation Leo". Now, obviously he didn't see what she was pointing out the first time around, but we could probably assume that from their point of view the sphere was in the general area that the constellation occupies in the night sky. Nice coincidence that the first attack on Earth by the Borg came from the same direction as the major battle between Starfleet and the Borg.
Trivia: The set that they use as sickbay on the Enterprise is the same set used as sickbay on Star Trek Voyager. In fact, the character of the holographic doctor is played by Robert Picardo, who starred as Voyager's holographic doc.
Trivia: The character of the nightclub owner is played by Ethan Phillips, uncredited, who starred as Neelix for 7 years on Star Trek Voyager.
Trivia: Watch the LCARS displays very carefully when Picard, Worf, and Lt. Hawk are reprogramming the maglock controls. Those with a careful eye can spot that one of the maglocks is the infamous AE35 unit, a tip of the hat to 2001: A Space Odyssey.
Trivia: When Dr. Crusher is moving everyone out of sick bay when the Borg are about to break in, she calls for the holographic Doctor. She tell him to distract the Borg long enough for them to escape. He says "I'm a doctor, not a doorstop", which was a nice salute to a line often said by Dr. McCoy (which the Doctor also used in the Star Trek: Voyager TV show).
Trivia: The missile silo scenes were filmed at the Titan Missile Museum in Green Valley, Arizona. It is a decommissioned site and the only Titan missile complex open to the public. In order to get the shot of the launch they lowered a camera down the length of the actual missile on cables. Members of the crew arrived weeks early to get exact measurements of the warhead so they could build the cockpit "capsule" to fit over it. The money Paramount paid to use the site was used to build the new Welcome Center.
Trivia: Not strictly a "movie mistake", but interesting to note. On the DVD commentary, Jonathan Frakes says repeatedly that the gun used by Picard in the holodeck scene is "a period German submachinegun". It is, of course, a Thompson M1928, possibly the most American submachinegun of them all. (00:51:45 - 00:52:20)
Trivia: Not exactly a mistake, but when the Vulcans land, Cochrane says "My God, they're really from another world!" I guess no one mentioned to him that the lady he tried to seduce and has been helping him the whole time is too. Though her father was human, Troi was born and raised on Betazed.
Trivia: Paramount Pictures took out ads in industry publications lobbying for Star Trek: First Contact to be nominated at the Academy Awards in various categories: including, prominently, Patrick Stewart for Best Actor. This was considered a gutsy move as acting nominations in "genre films" such as sci-fi, fantasy, and horror were extremely rare, especially at the time. Ultimately, the film was nominated for Best Makeup.
Answer: The borg took control of specific areas of the ship as part of their plan. This included deflector control and the shuttle bay.
My mistake. The main shuttle bay is around decks 5 and 6. The Borg didn't take control of those decks until after the beacon was destroyed.