The input locations dataset does not have a spatial reference. When this happens, the locations will obtain the spatial reference from the input raster, or rasters.
If only one raster is being sampled, the locations are assumed to be in the same spatial reference as the raster from which the values are being extracted. If multiple rasters are used, during execution the location input will use the spatial reference from each of the rasters, accordingly. This may lead to different results than expected, if the spatial reference of the input rasters vary significantly.
Before executing this tool, first use the Define Projection tool to define the correct spatial reference for the input locations dataset.