Here are a few I can think of after watching it a couple weeks ago:
Why did they send a cargo ship in the first place to answer a distress call, when no one aboard the ship was experienced in these matters?
Why did they let Kane explore the hole in the ship in the dark, without at least knowing more about where they were?
Why did Kane screw around with the egg, knowing that there was movement inside?
Why did Ash let Kane back on the ship with the facehugger attached to his face, without going through the 24 hour decontamination period like Ripley ordered?
Why did they not freeze Kane once he was brought aboard the ship?
When the facehugger "disappeared", why did the entire crew essentially go back to normal, knowing something had to be wrong?
When the alien attacks Parker, why did he not use the flame thrower?
Then here are the plot holes in Aliens:
http://movieplotholes.com/aliens.html