Anion intercalation into graphite is a central process for energy storage in dual-ion battery cells. Electrochemical investigations show a strong kinetic hindrance of the intercalation process in the first charging cycle and less kinetic hindrance in subsequent cycles. In order to obtain information about the structure and properties of the graphite electrode during cycling and about the origin of the kinetic hindrance, we carried out an in-situ Raman spectroscopy study during the first and second charging/discharging cycle of a dual-ion cell. This cell consisted of a metallic lithium anode, a graphite cathode and a Pyr1,4TFSI/LiTFSI mixture as electrolyte. We show that the TFSI− anion intercalation is not fully reversible, implying that TFSI− anions remain inside the graphite matrix after completion of the first charging/discharging cycle. This is in contrast to the reversible intercalation/deintercalation of cations, like Li+ ions. Remarkably, the TFSI− intercalation leads to enhanced Raman signals, also in stark contrast to Li+ intercalation. We discuss the in-situ Raman spectra in terms of staging phenomena, mechanical strain formation, electronic charge densities, and defects. Furthermore, we show that intercalation-induced defects are self-healing over time. Our results suggest that there is an anti-correlation between the kinetic barrier for TFSI− intercalation in graphite and the number of defects.