Revealing mistake: In the deflector dish scene when Worf chops the Borg's arm off with his mek'leth, the blade obviously doesn't even touch the Borg. (01:09:45)
Revealing mistake: Outside Engineering when Data twists the neck of one of the Borg, one of his sleeves comes up and you can see where the make-up on Brent Spiner's arm ends.
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.