Sometimes, it's not the research methods or the data that are flawed, but the interpretation of the data.
It’s human nature to see what we’re looking for—whether it’s really there or not—and not see what we’re not looking for. Scientific truth sometimes falls prey to this tendency of ours, when scientists inadvertently leap to conclusions their research doesn’t really support.
For a classic (and literal) example of just such a logical “leap,” consider the story of Italian anatomist Luigi Galvani who, in 1871, poked a brass hook into one of the frog legs he was preparing for dissection. When he saw the leg jump, he wrongly attributed the phenomenon to “animal electricity,” a then-popular concept that animal tissues contained a reservoir of electricity that gave them life.
Actually, it wasn't the frog leg that had produced the electricity, but contact between the brass hook and the iron railing from which it hung—a misunderstanding not corrected until years later. Galvani didn't realize it, but he hadn't discovered proof of “animal electricity” at all. He'd discovered the battery.
Sometimes researchers will admit to other possible interpretations of their results, but mistakes are often lodged hopelessly where no one can see them (yet): within the dominant paradigm. All science is necessarily provisional; today's facts become tomorrow's fiction as new measuring tools, new discoveries, and new paradigms continually expand our knowledge and understanding.