I considered it a hole in the plot and even added it to IMDB's goof section once upon a time, but it makes no sense that Ripley finds his communication later and that he's surprised by it. If Burke was indeed interested in covering his tracks, destroying all evidence of his communication with the colony would have been the first thing he'd have done when the marines got there. You mean he really just "forgot" about all those orders and communiques and that they may have kept records? Seriously? In real life, a bureaucrat who got a lot of people killed and was interested in covering it up would have that as his number 1 priority.
Also as Gorman said to Ripley, the entire basis of their mission was that they had "lost contact with LV-426". That would mean they'd be more focused on figuring out what happened to the base's communication system in order to find out why that had happened. Instead, the marines becomes oddly obsessed with tracking down the colonists once they find the place empty and nobody even thinks to look for the communication center and see what went wrong with it. Had they done that, it would have been very obvious that the communication with Burke had initiated the whole disaster as the Aliens were destructive by not interested in destroying records, as Ripley proves later when she confronts Burke with the giant wad of paperwork.
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