Incongruence between morphological and molecular-based phylogenetic hypotheses has been reported across a wide range of taxa. Specifically, morphological and molecular hypotheses of squamate phylogeny have been consistently incongruent and have been notoriously difficult to reconcile. With the ever-rising popular view of the superiority of molecular data over morphological data, studies have been biased toward seeking explanations for homoplasy in the morphological data. We propose considering approaches that do not make a priori assumptions about the superiority of one type of data over another. We present two case studies using the proto-oncogene c-mos, as well as a large multi-locus dataset, to examine apomorphy distributions across hypotheses. This approach reveals novel insights into data incongruence currently plaguing squamate phylogeny, with direct implications for other scenarios of phylogenetic incongruence.