A few of those have crossed my mind since the movie came out, but have been filed under 'don't care'. The drill disrupting communications, Nero and crew being on Rhura Pente for 25 years, but the ship just happened to still be there when it was time to break out, the brewery/engine room, red matter, etc. This isn't one of those movies that I wanted tight story logic and scientific accuracy, it's sci fi, they can do whatever they wanted. I just wanted to be enterained for a few hours and the movie succeeded. Most movies could be picked apart for their flaws and if a movie was written to make perfect sense and timing, the movie would probably be pretty boring.