Probably one on the saddest parts is one of the voice overs at the end. A Fox News-sounding reporter is ranting that the Sam that made it to Earth is a liar or loon and should either be ignored or, if I recall correctly, put in prison. The fact that who's implied to be a major news personality (and probably with no evidence of his own) is siding with the corporation speaks volumes on how hard Sam's first few months or his whole life will be. He may very well spend his entirety of his short lifespan fighting corporate heavyweight lawyers, with his only support being sympathizers and their donations, only to finally expose them when the signs of him dying become apparent.
I also think they left two things ambiguous. (It's been 3 years since I watched this gem. Of course, I forgot If they really did it with both or just the AI.) If Gerty was just a simulated AI, I'd like to think that it was just the shoddy programming of a cheap, profits first corporation that allowed him to get around any instructions to stop Sam from doing "unprofitable" things. He also said his main job was to help Sam, so that suggests either what I just said or the full blown AI with the ability to make its own choices. I like the full AI theory more than the "rewrote its own programming" deal, as it suggests kindness even from a machine made by Evil Inc. rather than space magic in a very hard scifi film.
The other one is what position was the original, uncloned Sam in. Did he know about all those clones and volunteer his own DNA for quick clones and his family to record 3 years of messages to trick the clones? If so, would he support the one that made it back, or is the corporate moolah still blinding his ethics? What about if he was up there 3 years and didn't know that he was a template for the clones? If it looked like he might help the clone, would the company try to silence him some way? They aren't above murder. They just have to get creative when eyes are finally on their target. These questions really make you think "How would a real life company treat a similar situation?", and it hits home hard how something like BP would probably spends millions to cover it up, rather than face the world.