Heterostructures of topological insulators and ferromagnets offer new opportunities in spintronics and a route to novel anomalous Hall states. In one such structure, EuS/Bi2Se3, a dramatic enhancement of the Curie temperature was recently observed. We performed Raman spectroscopy on a similar set of thin films to investigate the magnetic and lattice excitations. Interfacial strain was monitored through its effects on the Bi2Se3 phonon modes while the magnetic system was probed through the EuS Raman mode. Despite its appearance in bare EuS, the heterostructures lack the corresponding EuS Raman signal. Through numerical calculations we rule out the possibility of Fabry-Perot interference suppressing the mode. Direct measurements of the magnetic system also eliminate room temperature ordering from suppressing the mode. We therefore attribute the absence of a magnetic signal in EuS to a charge transfer with the Bi2Se3. This could provide an additional pathway for manipulating the magnetic, optical, or electronic response of topological heterostructures.