Considering his erratic and odd behavior towards the end, I personally believe he was malfunctioning due to a conflict of orders.

He is ordered to protect the alien but in order to do so he has to eliminate the threat posed by the humans and since harming humans is probably a law for robots, it created a conflict. That being said, Bishop mentions the three laws as being fairly recent so who knows if the older model Ash actually had any programming with laws regarding humans safety and health.

Before Ash assaults Ripley, there is an odd laugh/ choking sound. That coupled with the head shaking and blinking does point towards damage or an internal programming conflict. The method he uses to kill Ripley has been the subject of much speculation. Many have pointed out that it's an inefficient way to kill her. Plus the obvious sexual overtones, (a rolled up porn magazine forced down her throat). It's also been pointed out, he's emulating the creatures he admires. Given that Ash serves as the Nostromo medic and is probably programmed with human anatomy you would think he would have used a quicker more efficient method, like breaking her neck. Ridley Scott in one of the director commentaries mentioned he wanted to imply that was the closest Ash ever came to sex. There are several scenes in the film where Ash is clearly irritated with Ripley. Ash was required to kill her after she discovered the special order, but he chose a slow intimate way of doing so.

Yeah for essentially a walking computer (which should be all about logic and efficiency) his method of killing was very slow and inefficient. His strength alone could have killed her instantly, which is another thing. His strength should have allowed to him forced that magazine down her throat easily regardless of her resistence yet she was able to resist somewhat. There is definitely some form of conflict or issue is going on with him, he was even leaking white fluid from his forehead before he attacks her.

Two other scenes that suggest Ash had his own motivations: When Parker attempts to save Ripley, instead of just knocking him away, he starts crushing Parker's collarbone. After Ash pointed out they are required to investigate the transmission and Parker says , "right, we're going in" Ash is looking daggers at Parker's back. This was his way of getting back at Parker for picking on him.

When Dallas is in the air shaft, and the alien is closing in, Ash looks smug, almost a look of satisfaction that Dallas is being eliminated. Different scripts imply that Dallas and Ripley had a relationship, even in the finished film, there is an intimacy in how Dallas and Ripley interact. I've wondered if Ash had mixed feelings towards Ripley and saw Dallas as a rival.

I suppose that is what makes it all so interesting, there is different ways to interprete the motivations of Ash and the situation.

Personally I prefer the malfunction angle as a robot should not have the chemistry and hormones necessary to be sexually frustrated. Though David's story tends to throw that out of the window what with his tears and clearly emotional outbursts.

Excellent point, one which opens another area of speculation: Are the synthetics in the Alien universe just mechanical constructs that mimic humans, or are they a type of artificial life? There are good arguments for both.

Well the working Joes definitely seem more mechanical but synthetics such as Bishop are more ambiguous, their insides are clearly not organic yet not metal or mechanical either, it is an interesting thing to speculate about. Eldon from the fire and Stone series was what is called a "meat construct" being an android that is apparently truly organic, hence why he was vulnerable to the black goo accelerant.

In one way I am glad its not all explained much as it allows room for thoughts about it, plus it adds another interesting mystery to the universe other than just the Aliens.

I wholeheartedly agree, fiction, (whether film, books or whatever), should make one think. I recall reading somewhere someone pointed out that the use of the words Alien or Aliens in the franchise titles, could refer to the synthetics as well. They are certainly "alien" compared to humans.

Curiously I find it makes the Aliens less alien, as Covenant showed that David created them, meaning their are human's "grandcreation" for a lack of a better word, it makes the universe seem smaller, at least in my opinion anyway. Even the space jockey became less alien and more "off-shoot human"

It is good that it makes us question everything, but it also adds frustration.

But I can appreciete that it shows how dangerous the androids are in they own right as they are often overlooked as if they just another tool of man, yet one of them has created a very dangerous threat to most organic life.