Using Sn-intercalated TaSe2 as a model system, we demonstrate the presence of structural heterogeneity captured by single-crystal X-ray diffraction (SCXRD) and scanning transmission electron microscopy (STEM) that eludes the routine characterization techniques of powder X-ray diffraction, Raman spectroscopy, and electronic transport measurements. From a single growth composition (1:1:2 Sn:Ta:Se), we obtained crystals diverse in stoichiometry and structure, with near-continuous intercalation for SnxTaSe2 from 0 ≲ x ≲ 1. Using SCXRD, we found global structural diversity, identifying three new structure types: Sn0.18TaSe2.0/Sn0.08TaSe1.96 (R3m), Sn0.16TaSe2.0 (P63/mmc), and Sn1.2TaSe1.9 (Fmm2). Using STEM, we observed local structural diversity, manifested as regions of highly variable stacking within a single crystal. In contrast, powder X-ray diffraction did not resolve all observed global structures. Raman spectroscopy was unable to distinguish between different structures or compositions in the standard measurement range. Electronic transport measurements showed consistent superconductivity and charge density wave behavior irrespective of Sn-intercalation amount. Our results indicate that routine approaches to characterization of intercalated transition metal dichalcogenides may be inadequate for capturing the diversity of this family of materials, highlighting the need for high-resolution structural characterization when examining the properties of van der Waals-layered compounds.