Here's why Ash uses a rolled-up magazine while trying to kill Ripley in Aliens is painted as a potential villain, which is seemingly confirmed in the finale when he appears to have taken off in the dropship without Ripley and Newt.
He reappears just in the nick of time to save the day, however, and is revealed to have been completely trustworthy. Henriksen himself decided to play Bishop as something of a naive teenage boy, who is endlessly fascinated by the world around him. Winona Ryder's Call is revealed to be an advanced, heroic droid in Alien: Covenant seems to have nixed that plan.
Ian Holm's reveal as an android comes late in the story and is something of a shock twist. Given the perverse sexuality of the various H.R. Giger designs in the movie, including the facehugger attack on John Hurt's Kane being a form of oral rape, it's little wonder Scott extended that subtext to Ash's assault on Ripley in Alien. This scene sees Ash attack Ripley when she learns of the company's plans for the crew and the creature, and he rolls up a pornographic magazine to shove it down her throat. The question, of course, is why he'd go through with such a needlessly elaborate attack, as given his strength he could just snap her neck.
This goes back to the Freudian, psychosexual themes that underpin Alien. On the surface, Ash could just be paying homage to the "perfect" creature he ires so much, with the magazine symbolizing the way the facehugger impregnated Kane. It's an illogical act, but the android is shown at this point in the story to be malfunctioning somewhat. There's also a more disturbing reason, which Ridley Scott has stated in several interviews and commentaries for Alien.
In Scott's mind, Alien's Ash might be an android but he has to process complex emotions he doesn't always understand. Scott believes Ash is sexually attracted to Ripley but lacks any physical capabilities to do anything about it or the emotional capacity to understand it. The magazine is a phallic symbol in this attack, with the android essentially trying to commit oral rape. Luckily, Parker and Lambert turn up in time to rescue Ripley, managing to disable Ash and later interrogate him about the creature.
