  Topological transport phenomena in magnetic materials are a major topic of
current condensed matter research. One of the most widely studied phenomena is
the ``topological Hall effect'' (THE), which is generated via spin-orbit
interactions between conduction electrons and topological spin textures such as
skyrmions. We report a comprehensive set of Hall effect and magnetization
measurements on epitaxial films of the prototypical ferromagnetic metal
SrRuO$_3$ the magnetic and transport properties of which were systematically
modulated by varying the concentration of Ru vacancies. We observe Hall effect
anomalies that closely resemble signatures of the THE, but a quantitative
analysis demonstrates that they result from inhomogeneities in the
ferromagnetic magnetization caused by a non-random distribution of Ru
vacancies. As such inhomogeneities are difficult to avoid and are rarely
characterized independently, our results call into question the identification
of topological spin textures in numerous prior transport studies of quantum
materials, heterostructures, and devices. Firm conclusions regarding the
presence of such textures must meet stringent conditions such as probes that
couple directly to the non-collinear magnetization on the atomic scale.
