The Yerushalmi in Pesachim has a machlokes whether karmis, some type of millet-like grain, can become actual chameitz or not (similar to the more well known machlokes Rabbi Yochanan ben Nuri and Rabbanan by millet and rice). Asks the Yerushalmi (17a), why not simply test it and see? The gemara answers that a test was in fact done and what the results were is precisely the point of machlokes.
I seem to recall the Yerushalmi in other places asking similar questions when a debate focuses on issues of fact rather than interpretation – if all that is in question is fact, then we should be able to settle the machlokes. Bnei yeshiva usually operate under a similar assumption that "there cannot be a machlokes in metziyus" and all issues boil down to conceptual disagreements. Interestingly, I cannot recall offhand anywhere that a similar question is raised in the Bavli, but if anyone remembes otherwise, let me know.