There is a fantastic article in the latest issue of Wired entitled, "Accept Defeat: The Neuroscience of Screwing Up." The article discusses, in a very readable way, the real-world problems of scientific research, and provides a neurological explanation for why researchers often make very-human mistakes when considering data and results that do not conform to their pre-existing expectations. Several historical examples are offered, ans research by psychologist Kevin Dunbar into the process of research illuminates how preconceived notions about what "should" happen often negatively impact the interpretation of unexpected results - often leading to a conclusion that there must have been a mistake, rather than considering alternatives. From the article:
Dunbar came away from his in vivo studies with an unsettling insight: Science is a deeply frustrating pursuit. Although the researchers were mostly using established techniques, more than 50 percent of their data was unexpected. (In some labs, the figure exceeded 75 percent.) “The scientists had these elaborate theories about what was supposed to happen,” Dunbar says. “But the results kept contradicting their theories. It wasn’t uncommon for someone to spend a month on a project and then just discard all their data because the data didn’t make sense.” Perhaps they hoped to see a specific protein but it wasn’t there. Or maybe their DNA sample showed the presence of an aberrant gene. The details always changed, but the story remained the same: The scientists were looking for X, but they found Y.
One suggestion for avoiding non-inquisitive thinking: diversity, primarily of attitude and scientific background. That is, individuals who don't already "know" the material at hand may well bring a fresh perspective. In addition, outsiders are often less constrained by what is "settled" in the field in question, and might be more willing to challenge orthodoxy. I recall in When Life Nearly Died, it took several non-paleontologists (I believe their background was physics, though I can't recall for sure) to break down the century-old taboo against suggesting a meteor might have caused a mass extinction of the dinosaurs.
I highly recommend you read the whole thing, both for the discussion of the research into the scientific processes of research, as well as the neurological discussion into how the brain handles disparate data. Great stuff, and one of the best articles I've read in Wired in some time.