Question: Were the scientists involved really concerned about igniting the atmosphere?
Question: Why are most of Robert Downey Jr.'s scenes shown in black and white?
Answer: The black and white scenes are shown from the perspective of Lewis Strauss (Robert Downey Jr.), whereas the scenes in colour are shown from Oppenheimer's perspective.
Answer: The short version is "no, not really". Much like in the film, the possibility was considered, a lot of calculations were done, and it was agreed by everyone privy to them that the chance was basically zero. Also like in the film: "what do you want from theory alone?" - it couldn't be guaranteed to be absolutely zero, but then the chance of almost anything happening is never absolutely zero. A 1946 report by three of the scientists stated: "whatever the temperature to which a section of the atmosphere may be heated, no self-propagating chain of nuclear reactions is likely to be started. The energy losses to radiation always overcompensate the gains due to the reactions."