Organic and inorganic materials are more and more frequently combined in high-performance hybrid electronic and photonic devices. For such multilayered stacks, the identification of layers and interface defects by depth profile analysis is a challenging task, especially because of the possible ion beam induced modifications. This is particularly true for perovskite solar cells stacks that in a mesoscopic structure usually combine a metal electrode, a mesoscopic conductive oxide layer, an intrinsically hybrid light absorber, an organic hole extraction layer and a metal counter electrode. While depth profile analysis with X-ray photoelectron spectroscopy (XPS) was already applied to investigate these devices, the X-ray and ion beam induced modifications on such hybrid layers have not been previously investigated. In this work we compare the profiles obtained with monatomic Ar+ beam at different energies, with the ones obtained with argon ion clusters (Arn+) with different sizes (150<n<1000) and energies (up to 8 keV). A systematic study is performed on full mesoscopic perovskite (CH3NH3PbI3) solar cells and on model hybrid samples ((FAxCs1-xPbI3)0.85 (MAPbBr3)0.15)/TiO2). The results show that for monatomic beams, the implantation of positively charged atoms induces the surface diffusion of free iodine species from the perovskite which modifies the I/Pb ratio. Moreover, lead atoms in the metallic state (Pb0 ) are found to accumulate at the bottom of the perovskite layer where the Pb0 /Pbtot fraction reaches 50%. With argon clusters, the ion beam induced diffusion of iodine is reduced only when the etch rate is sufficiently high to ensure a profile duration comparable with low-energy Ar+. Convenient erosion rates are obtained only for n=300 and n=500 clusters at 8 keV, which have also the advantage of preserving the TiO2 surface chemistry. However, with argon cluster ions, Pb0 particles in the perovskite are less efficiently sputtered which leads to the increase of the Pb0 /Pbtot fraction (up to 75%) at the perovskite/TiO2 interface. Finally, ion beam and X-ray induced artifacts on perovskite absorbers can be reasonably neglected for fast analysis conditions in which the exposure time is limited to few hours.