I'm going to get flamed for saying this but I think Ridley is feeling embarrassed because the film isn't as epic and scary as he was promising it would be. Is it a failure? Not by any means - a lot of people actually love it and it's doing well in the box office considering it's an R-rated film. But by disassociating the film with the Alien franchise, he doesn't have to feel as embarrassed about it's relation to the franchise.
But let's be honest - if he really didn't want it to have anything to do with the franchise, why the f**k would he include those few elements?
First I remember him saying that this isn't the film that ties directly into Alien, but it is a prequel. Then the cast were switching back and forth between it being a prequel and not being a prequel. Then they were all saying it's a prequel but not in the strict sense of the end scene tying in with the beginning of Alien. I don't even know if they're sure what to call it anymore.
So Ridley, this isn't a prequel. Then what the f**k was that Space Jockey chair and suit doing there? What the f**k was that mural and Deacon chestburster all about? Why were you trying to rival the chestburster scene? Why was Weyland involved? I could go on but I'm tired of this crap.