Philosophical discussions of disagreement typically focus on cases in which the disagreeing agents are aware that they are disagreeing and can pinpoint the proposition that they are disagreeing about. Scientific disagreements are not, in general, like this. Here we consider several case studies of disagreements that do not concern first-order factual claims about the scientific domain in question, but rather boil down to disputes regarding methodology. In such cases, it is often difficult to identify the point of contention in the dispute. Philosophers of science have a useful role to play in pinpointing the source of such disagreements, but must resist the temptation to trace scientific debates to disputes over higher-level philosophical accounts.