Other mistake: Unfortunately the whole basis of the show is one big factual error. Throughout the series we see that Red Dwarf sustains damage from collisions, explosions, and so on. Most important of all, the rocket engine nozzle - surely made from the strongest materials available - has been punctured by some kind of impact. The systems require constant maintenance by humans (painting, repairs, etc), so skutters are not enough by themselves. So, we know that Red Dwarf is not made of some sort of fictional, indestructible materials, it is made of the kind of metals, plastics and other construction materials we build space shuttles and the like out of nowadays. So, after three thousand - never mind three million! - years the whole ship would be a clump of useless, corroded junk. The rubber and plastics in seals, electronic components and furniture would have crumbled to powder. The electronics themselves would have failed after a few hundred years at most. Metals in contact with liquids in pipes or reservoirs would have oxidized, and even the oxygen in the air would have been corrosive after that amount of time. Red Dwarf is not immune from the effects of long term decay and deterioration - if it were when Lister was released from stasis he would have found rooms full of relatively intact dead bodies instead of piles of crumbled dust. After three million years in space Red Dwarf would have been a pile of scrap, fatal to anyone going near it; subject to slow, subtle but constant radioactivity in space, after three million years it would be hotter than the inside of a working reactor.
Red Dwarf (1988)
1 other mistake in show generally
Plot hole: Cat wasn't manufactured by the Jupiter Mining Corporation and had no connection with them, being born three million years or so after they lost control of Red Dwarf. The takeover by M-Corp would mean nothing to him. Why, then, does he become invisible to Lister?
Suggested correction: Cat was a descendant of the cat Lister brought aboard Red Dwarf. Would it be possible that the new owners might have stricter security controls, and Lister was sent to Stasis for a different reason?
Inventing Deux ex machina explanations for a plot hole doesn't make it any less of a plot hole. M-Corp erases all of the Jupiter Mining Corporation's equipment, personnel and infrastructure from Lister's life. In no way is Cat a part of that. He has no connection at all to the Jupiter Mining Corporation, and until he meets him in Episode 1 no connection to Lister, either.
If M-Corp only erased JMC equipment from Lister's life, then Kryten, who belongs to DivaDroid and not the JMC, wouldn't have disappeared either. He disappears as he doesn't belong to M-Corp, not because he belongs to the JMC. Cat has no connection to M-Corp, as he wasn't a part of the JMC (as you pointed out), and is therefore erased for Lister.
Trivia: "Meltdown" was originally planned to be the first episode of Series IV of Red Dwarf. However, the militaristic tone of this episode - and in particular Dave Lister's strident anti-war speech near The End of the episode - meant it fell foul of the BBC censors. The original planned transmission date (Feb 14 1991) coincided with the outbreak of "Operation Desert Storm" - the Gulf War...and the BBC felt that an "anti-war" episode of Red Dwarf would be inappropriate for a country at war with Iraq.
Chosen answer: In-universe, after leaving Red Dwarf after his first appearance, Kryten managed to crash Lister's space-bike into an asteroid. Lister found his remains and decided to rebuild him, however, due to the high level of damage and Lister's questionable repair skills, he was unable to recreate Kryten exactly, leading to changes in appearance, personality and accent. In reality, the original actor wasn't available, coupled with presumably practical concerns about one-off makeup as opposed to makeup for a regular cast member, so some visual changes were made.
Suggested correction: We don't have enough detail on what the ship is made out of. It taking damage doesn't mean it's made from current materials; it could use new materials with unknown properties. Eg, when the polymorph goes through a metal pipe, the tap distorts then reshapes. Seemingly impossible, but it happens. Rubber and plastics may not pulverize. Metals could be oxidation resistant. Advanced filtration might keep air fresh indefinitely. Technology that we can't imagine today keeps everything working and safe.