Science is no more immune to conceptual error and confusion than any other forms of intellectual endeavour. The history of science is littered with the debris of theories that were not simply factually mistaken, but conceptually awry.M.r. Bennett and p.M.S. Hacker
In short, conceptual entanglement can coexist with flourishing science. This may appear puzzling. If the science can flourish despite such conceptual confusions, why should scientists care about them? Hidden reefs do not imply that the seas are not navigable, only that they are dangerous. The moot question is how running on these reefs is manifest. Conceptual confusions may be exhibited in different ways and at different points in the investigation. In some cases, the conceptual unclarity may affect neither the cogency of the questions nor the fruitfulness of the experiments, but only the understanding of the results and their theoretical implications.
Bennett, M.R. and Hacker, P.M.S. (2003). Philosophical foundations of Neuroscience. Blackwell Publishing.