The topological Hall effect is an exotic manifestation of the coupling between magnetic skyrmions and electronic currents. The proposal that this effect can be used to detect isolated skyrmions has hardly been tested directly, especially in the recently introduced multilayer films. We combine transport and magnetic imaging to study this relationship in such a film, which hosts Néel skyrmions. We demonstrate an intricate correspondence between skyrmions and topological Hall resistivity over a wide range of temperature and magnetic field. In particular, using our newly developed model for the stray field from skyrmions, we show clustering of skyrmions into worm-like structures carrying a considerable topological charge. We also measure a topological Hall resistivity much larger than the prevailing theory predicts for the observed skyrmion density. We suggest that band structure plays an important role in the skyrmion–current coupling, with implications for the impact of the Berry-phase of skyrmions on charge carriers.