Nothing on a giant spaceship could survive after three million years, why have they not realised that Holly and other systems on Red Dwarf would fail, and eventually disintegrate LONG before 3 million years had passed?
Maybe they have realised and don't care? It's a sitcom made for enjoyment, not to be picked apart at.
Anything that bothers you so much about the science of it, just remember that it's set hundreds of years in the future, so maybe the technology is superior in those days and has found a way.
Either that, or don't worry about it at all and just laugh at the jokes.