Debates over the interpretation of quantum theory have evolved dramatically from the inception of the theory in the late 1920s to today. Before World War II, epistemology was part of the game in physics and the debates between Einstein and Bohr were considered quite naturally as part of the development of physics. After World War II these debates were revisited but given a new slant, namely that of a philosophical controversy, beyond physics, which did nothing to attract young physicists to work on the subject. Later, after Bell’s theorem and professional changes in the status of foundational issues among the physicists in the early 1970s, the nature of debate changed once again and some hitherto controversial subjects became part of mainstream physics. The effective interaction between theory and experiments, which became current from the 1970s on, did not, however, eliminate the philosophical implications of this controversy, as can be seen from the proposal made by the physicist and philosopher Abner Shimony towards the development of an experimental metaphysics. Through a historical reconstruction of these debates we will see that even the lexicon of this debate was a controversial matter. Is there really a controversy? Is it philosophical or scientific? Answers to these questions were not independent of the characters and their projects. However, regarding the whole period under consideration, we will try to evaluate to what extent philosophy is ultimately responsible for the debates over the interpretation of quantum theory. Our conclusion is that in addition to epistemological and ontological issues, related to locality, realism, and separability, the history of these debates has brought to the history of physics a case of underdetermination of theories by empirical data. This is a thesis about the nature of science which was first suggested by Pierre Duhem and resumed by Willard Van Orman Quine. This conclusion, drawn from the history of these debates, has far reaching implications for the current practice of physics, its teaching, and its public image. We have termed it “an inconvenient truth” (Greca & Freire, 2013).