The Cathars
The crusade against them is a certain, well-documented historical fact. More recent scholarship has raised a genuinely serious question about the religion itself: whether an organised 'Cathar church' actually existed as such, or whether it was substantially constructed by the standardised questions inquisitors themselves used when interrogating suspects.
R. I. Moore, The War on Heresy (2012); Mark Gregory Pegg's scholarship questioning the existence of an organised Cathar church
A medieval dualist religious movement in southern France against which the Catholic Church launched a major military crusade in the thirteenth century.