There were only two facehuggers - the one that got Ripley and the one that got the dog/ox (depending on what version of the movie you saw). It was proven in the autopsy that Newt died from drowning and did not have an alien inside of her and Hicks died from part of the ship crashing into his cryo-tube.

But still, it didn't make any sense where the eggs came from. I agree with that.
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Art thou the bringer of ruin? Art thou the holy one?