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Topological materials are of high interest due to the promise to obtain low power and fast memory devices based on efficient spin-orbit torque switching or spin-orbit magnetic state read-out. In particular, sputtered polycrystalline Bi$_x$Se$_{1-x}$ is one of the materials with more potential for this purpose since it is relatively easy to fabricate and has been reported to have a very high spin Hall angle. We study the spin-to-charge conversion in Bi$_x$Se$_{1-x}$ using the spin pumping technique coming from the ferromagnetic resonance in a contiguous permalloy thin film. We put a special emphasis on the interfacial properties of the system. Our results show that the spin Hall angle of Bi$_x$Se$_{1-x}$ has an opposite sign to the one of Pt. The charge current arising from the spin-to-charge conversion is, in contrast, lower than Pt by more than one order of magnitude. We ascribe this to the interdiffusion of Bi$_x$Se$_{1-x}$ and permalloy and the changes in chemical composition produced by this effect, which is an intrinsic characteristic of the system and is not considered in many other studies.