There is a 42 year gap between A:I and Aliens. Everything is entirely plausible and easily explained at this point. A sequel may muddy things up, but as it stands, A:I fits rather neatly into the continuity.
1. Burke had plenty of reason to lie, especially if he uncovered something about the events of A:I. If someone else in the company was able to connect the dots with the loss of the Nostromo and the space station years later, then of course he is going to drum up something. It's his character. He's blind with greed and ambition.
2. The writers gave an explanation for Amanda's inclusion. She was looking for information about her mother. That's all the reason that is needed. As for no one looking into Amanda's reports, we don't have any evidence that is clear cut at this point that she survives to do that. Again, Burke isn't trustworthy.
3. If only a few corporate people were involved, maybe they thought it more prudent to just cover the Nostromo incident up rather than get exposed to lawsuits, fines and imprisonment.
4. It can't shit all over Ripley's character. Ellen is incredibly smart, but not all knowing for starters(egg on Sulaco, xeno in the Narcissus). Not checking into a very likely story that her daughter was dead 57 years later hardly sticks out as a bad characterization. If anything, blame Cameron for not showing that. It's just not a hard thing to believe someone died in their 60s. Isn't it only around 30 days before she's back on LV-426? Maybe it was something she was trying to look into. Bureaucracy and all that. On top of that, Van Leuwen admits there is a colony on LV-426. The fact that aliens aren't running amok on Earth or in the news and she knows a colony is there, probably made her realize that W/Y wasn't on to anything at that point, or that the creeps involved are long dead. Never mind that she is an emotional and mental train wreck at this point.
5. A recent novel contradicts the notion that W/Y doesn't know something is on LV-426.
I think he refers to Ripley's characterization as in she didn't check out Burke's information on Amanda for herself or search for any mention of aliens.
I just don't see how anyone can take a hardline stance that A:I screws up continuity. I'm open to evidence to the contrary. Good night