In Alien, Ash is trying to kill Ripley. By doing so, he rolls a magazine to a pipe and puts it over her mouth. And that's it. She has both her arms, hands, legs and feet free. Her nasal passages were also free, so she could breathe just fine.

Since Ash is a (GOD DAMN) robot, did something in his programing go wrong during his murdering spree?

Just had to rewatch the scene as I didn't remember it at all (it's been more than ten years since I've wachted the movie). It's indeed weird, like he's generally acting up and trying something completely pointless.

It's the same MovieLogic that lets you kill someone in ten seconds with a pillow.

I think he was trying to force the magazine down her throat in order to choke her to death, but it also always seemed to me like he was starting to malfunction at that point.

Pretty sure this is exactly it. Also think this is what's going on as well, since he's actually so much stronger than her that it makes no sense for him to try to kill her in that fashion when he could probably have just easily choked the life out of her with his hands.

He didn't appear that strong when Parker slapped Ash's head off with a fire extinguisher. :P

According to the director, there is a Freudian explanation:

http://alienexplorations.blogspot.ch/1979/10/unravelling-of-ash.html

That's exactly what's happening.

Also of note, is that the entire movie has a theme of sex, pregnancy and rape, and that scene has a few layers to it as well. Ash is using a porno mag forged into a phallic shape to assault Ripley. There's a lot out there on the symbolism and I think Dan O'Bannon talked about it and touched on that scene in particular.

Edit: Or awalterj could post a link that explains it better than I could while I was trying to think of how to type it up.

Well, If memory serves, that's also the scene where he grabs a handful of Parker's chest and damned near rips it out, no?

Yes sir

Interesting. It's like the sexual subtext is subconsciously obvious to (nearly) everyone but doesn't necessarily appear like a genuine explanation for his behaviour in the scene. Good stuff.