Plot hole: In multiple scenes in the movie the starship is in a gentle rotation which allows 1G gravity on the ship. When the power to the propellant is cut the rotation stops and gravity is lost. Such a design for a starship doesn't make sense as the entire structure could be put in a continuous motion, as is indeed done with many probes today without requiring the continuous addition of power. Even if this design was chosen with part of the structure fixed and party of it moving around it still seems unlikely that the rotating part would come to a grinding halt within seconds (if it did, the friction of the structure would be huge, requiring enormous levels of energy to keep it moving) The only reason the movie chooses this unlikely design is to integrate the crucial shot of Aurora floating out of the pool when power is first lost.
Suggested correction: There are parts spinning with different speeds and directions. Spinning an entire solid ship wouldn't allow for things like that. Regardless, we can't say which starship designs make sense or not. The ship has a reactor with seemingly endless energy, so powering the rotation is not a problem. The sudden stop is because whatever spins the ship has lost power. If you try to turn an unpowered motor or engine, especially if geared, you will feel resistance because the mechanism is acting as a brake.
Plot hole: Gus wakes up and doesn't realise initially that he's seriously ill, although he knows he's not right. When Jim woke he was given a full body scan to check his health minutes after waking, so surely Gus must have had the same scan? When all his medical problems would have been identified. So he'd have known he was very ill minutes after waking.
Suggested correction: Minutes after waking there was nothing wrong with his body yet, his body started to deteriorate rapidly afterwards.
How do you know nothing was wrong with him minutes after waking up?
Because he got a full body scan like you said and nothing came up. The first sign of symptoms he shows is after they enter the bridge (or command center) and he dismisses it as something common. Before that he shows no sign of any medical problems.
That's the mistake here - he should have had a body scan on wake-up. So did he develop multiple medical issues in the pod because his pod function was affected by the central computer being damaged by the asteroid strike? Which would fit as his pod woke him up early, a built in safety feature perhaps so people don't die in their pods? Maybe his pod wasn't working right for 2 years, so slowly damaging his body? So the wake-up body scan should have detected his multiple issues! He couldn't go from healthy to over 600 disorders in a day.
I'm not sure the pods are sensing anything, they're essentially freezers, but without freezing you. The finger connections are not sensing anything from a person in the pod as there's nothing to sense, as people are dormant. It only senses vital signs when people are woken up. So Gus blaming his pod for his medical issues is inaccurate surely? A movie mistake?
The malfunctioning pod caused his medical issues. It keeps them in cryogenic stasis. We don't know exactly how they work of course but it is more than just sensing. Basically the people inside the pods are kept dead, but the pod manages to halt any deterioration of the cells. Imagine that going wrong and the pod isn't able to keep the cells in check. Just like when exposed to high levels of radiation the cells have been damaged but there won't be any signs immediately. Only after a few hours the cells will start to break down.
He developed several severe medical issues after being woken up too early in a pod that was malfunctioning. This is fictional, future technology and we have no idea how it works, but I think its safe to assume that the pod has to keep the entire body in check during cryosleep, and if the pod malfunctions it could cause all kinds of problems, both directly and later on. If it works on a molecular level than no issue can be detected for quite a while before problems start to show, much like with radiation poisoning when cells suddenly and rapidly start dying whilst hours or even days before you feel fine.
Plot hole: Starship Avalon is supposed to be an extremely highly advanced spaceship with capabilities well beyond current technology. Because the pods are supposed to be "fail-safe"/fail-proof, no provisions whatsoever were made to detect a pod failure or sound an alarm - a severe "oversight" for the ingenious people/engineers behind its creation. There apparently are sensors everywhere to automatically activate certain things (e.g, doors, holograms) when a passenger or crew member enters or approaches yet some of the things the holograms said indicated they were preprogrammed to say certain things, even though those things weren't appropriate under the circumstances. For example, soon after Jim entered the room for Learning Group 38, a hologram said, "Hello, passengers. Will you all take a seat." Surely there would be a sensor to detect that all the passengers supposed to be present were or know that almost all were not! The holograms/androids could not respond to some anomalies.
