1979's Alien was Sigourney Weaver's breakout role, but her debut as Ellen Ripley quickly established her as a character who is not without her flaws. Although she doesn't appear in every movie in the franchise, Ripley remains the most beloved Alien protagonist. This is all despite the second of Weaver's four Alien movies being largely regarded as much worse than the first two.
Ripley is remembered for her no-nonsense attitude, talent for improvisation, and innate leadership abilities. Her journey through the franchise is filled with twists, turns, and scrapes with death, which makes it difficult to remember her in anything but a positive light. Unfortunately, there is at least one notable instance where she was incredibly inconsistent, and it's pretty hard to defend.
The scene that sets up Ripley's hypocritical moment in Alien
When Kane (John Hurt) has a facehugger latched onto him after checking out the Xenomorph eggs, Ripley is the only member of her crew to raise concerns about allowing him back on board the ship. Everyone else is more concerned with Kane's condition. While this is a perfectly understandable thing to be worried about, Ripley is also correct in saying that the crew had already broken quarantine and that bringing an unknown organism aboard could leave everyone even more defenseless.
The dilemma becomes a matter of head over heart, and Ripley is quickly outvoted as Kane is brought inside as the crew looks for a way to free him from the alien threat. Ripley's caution ultimately turns out to be warranted, as she becomes the only survivor after the Xenomorph bursts from Kane's chest and goes on a bloody rampage through the ship. Hindsight is 20/20, but the relevance of Ripley's objections is retroactively increased tenfold in the wake of all the death.
This isn't the scene where Ripley acts hypocritically. She acts very reasonably and tries to encourage everyone to follow protocol. She's acting as a leader should and trying to make everyone think objectively, rather than acting out of fear and making decisions they might come to regret down the line. Of course, they did come to regret ignoring Ripley, but at least we got an awesome sci-fi franchise out of their reckless attitudes.
Ripley was far more careless with quarantine procedures later in Alien
I remember being very proud of Ripley when I first watched Alien for her determination to follow procedure in the face of a scenario that would have made it easy to act emotionally. While her crew ended up ignoring her main point of trying to keep everyone safe, it can't have been easy to say that Kane should effectively be left outside to die.
However, immediately following a later scene — that shows Ripley criticizing the ship's science officer to his face for his decision to open the door for Kane — I was forced to judge her more harshly. After being summoned to the med bay to see that the facehugger had unlatched itself from Kane's face, Ripley does her own ignoring of what is surely another quarantine procedure.
Ripley does tell Dallas (Tom Skerritt) to be careful while entering the room to locate the missing facehugger, but she also makes no effort to reduce the possibility of its escape. In fact, there is a long, tense shot that lasts over a minute, showing Ripley edging slowly into the room with the door wide open behind her. After her evident annoyance at being ignored about quarantine procedure earlier in the movie, this shows a strong degree of inconsistency in her character.
Although she wasn't to know this at the time, standard facehuggers in Alien lore are only capable of infecting one host before perishing. So, even if the parasite in question had escaped, it wouldn't have been able to plant a Xenomorph baby in anyone else. Still, its highly corrosive blood isn't exactly without risk.
Lapses in judgement make the Alien franchise more entertaining
I know exactly why Ridley Scott made the directorial decision to include that lingering shot of the open med bay door. It was so we'd all be looking at it and panicking that the missing facehugger would escape. It certainly worked for me, so I see the hit that Ripley's character takes as a result as a sort of necessary downside of the filmmaking technique.
Besides, movies like Alien would be pretty dull if all the characters constantly made good decisions. For example, if Ripley had managed to convince everyone to leave Kane outside, the Xenomorph growing inside him would invariably have burst out of his chest on the planet's surface, making it much easier for the ship to take off and escape. If anything, the med bay scene is a rare example of an Alien character getting away with a huge error in judgment.
Ripley's failure to close the door behind her in the med bay wasn't the first mistake an Alien character made, and it certainly wouldn't be the last. Even Ripley herself makes a similar error in the 1986 sequel, Aliens. Putting Newt (Carrie Henn) to bed in a lab full of "dormant" facehuggers is a terrible idea, but it also resulted in one of the best fight scenes in the entire Alien franchise.