Question: When Ripley and Newt are trapped in the Med Lab with face huggers (thanks to Burke), Ripley wakes Newt and tells her they are in trouble (which they are). But how does Ripley know this? She hasn't seen the face huggers at this point.
Answer: The two face-huggers were being kept in glass containers. When Ripley woke up, she saw that the jars had been tipped over, were empty, and the creatures were loose; Burke had released them, took her weapon, and locked the doors, while she was sleeping. He also turned off the CCTV monitors.
Answer: The marines worked for the Weyland-Yutani company. They're basically a corporate para-military. Burke was in charge of the operation, so he presumably assumed they, and also Bishop, the company android, would follow his orders, not fully knowing the circumstances. Burke probably intended that most of the marines would also be "infected."
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