In early June 2015 the Ion and Electron Sensor (IES) on board the Rosetta spacecraft (SC) observed troughs in the ion measurements at about 200 km from the comet. The troughs coincided with measurement results of two other instruments on board Rosetta: the peaks of the neutral gas density measured by the Rosetta Orbiter Spectrometer for Ion and Neutral Analysis (ROSINA) and the peaks of the electron density measured by the Langmuir and Mutual Impedence Probe Instruments, (LAP and MIP) and the most negative levels of the Spacecraft potential also measured by LAP. We propose that the dips in the ion measurements are the result of charge exchange reactions between the ions and the neutral population emitted by the comet nucleus. Measurements from the Ion Composition Analyzer (ICA) on board Rosetta show that these ions are mostly water ions.