That film is just fiction. I don't think anybody in the team has claimed any of it is true. Like all good science fiction they take real science and change it a bit to make it more entertaining. Nothing wrong with that but you shouldn't confuse it with theories put forward by real researchers.
I supose this new "mockumentary" trend can get quite confusing for people who don't have experience from the academic world.
The supernatural is a force in the world that can break the laws of nature. I'm sure, (quite positive) there are aspects of the laws of nature we haven't fully understood yet. So far we agree. To take flaws in our mathematical models of nature assume that the laws are being deliberatly broken is just dumb and not any evidence at all for the supernatural. Whether you'd like to call these anomilies we haven't understood yet for spirits or dieties is of no consequence. The important thing is what you believe they can and can't do.
All it means to be an atheist is that one doesn't believe that there is a force in the world that can break the laws of nature.
I hope you don't believe that the spirits can comunicate with us because even here there's been masses and masses of research and science have come up with nothing. Assuming from this that all spirits are shy in the presence of scientists is a bit naive, wouldn't you agree? We do know how neurons send messages within the brain so we can measure any thoughts being transfered from an external source and it just doesn't happen. We just haven't figured out exactly how complex thought works mechanically or chemically.
Our brains are very fast at working out stuff from incomplete evidence and sketchy data, (often leading to false conclusions). That is the strength of our brains, that's why we are the creative machines in the world. It's easy to understand how we can feel like we are getting external signals to it, but I'm certain it has never happened. Our brains can't really distinguish between what is internal thought and what is things comming in from outside. We have use various clues to distinguish them. If we can't see the clues then it can be easy to get the feeling it's god/spirits.
Human perception was part of my degree so I can pull research out my ass to back my shit up all day.