The input point feature class contains duplicate points, and the duplicates have been removed for analysis. Note that there is no way to control which points are used or removed if there are duplicates.
This is an automatic process when duplicate points are encountered. You should carefully analyze the results to make sure the output is what you expected. If you think your data contains duplicate points and want to remove them, first you need to determine where the duplicates occur. Try using the Add XY Coordinates geoprocessing tool to sort the point locations.