You guys remember that promotional video of Shaw talking about her project to Peter Weyland? You could see the Yutani icon all over the place in that video. My money is on the idea that Yutani was following Shaw and as soon as Shaw takes off from LV-223, we see a Yutani ship following her as well. Remember, at some point before the events of Alien, the 2 companies have to merge. That is a fact.