Here, we report a magnetotransport study of high-quality SrRuO3 thin films with high residual resistivity ratios grown by reactive oxide molecular-beam epitaxy. The transverse resistivity exhibits clear anomalies which are typically believed to be signatures of the topological Hall effect and the presence of magnetic skyrmions. By systematically investigating these anomalies as a function of temperature, field, film thickness, and excitation currents we verify that these anomalies originate from a two-channel anomalous Hall effect arising from magnetic inhomogeneities in the samples and not from an intrinsic topological Hall effect. Using a combination of magnetic circular dichroism, scanning transmission electron microscopy, x-ray diffraction, and magnetotransport, we discover that strain relaxation effects in the films are the origin of these inhomogeneities. Our results shed light on the recently reported Hall effect anomalies in SrRuO3 thin films and heterostructures and provide an approach to determine whether such anomalies arise from an intrinsic topological Hall effect or from extrinsic mechanisms. © 2020 American Physical Society.