The points are converted to raster internally. You probably have a resolution large enough that two or more points are in a single cell. Since the cell can only be 1 value it takes the point with the highest feature ID. This is discussed in the tools documentation under "Usage".
You should note that since you are using points, not polygons, your really just sampling the input value raster. It's not actually calculating a mean value. You should see that Min, Max, and Mean are all the same value. If you were to buffer the points and use those polygons as the zone features, then you would get a real mean calculation.
Best,
Eric