The format of the Raster (File GDB Raster dataset, TIFF, IMG, etc)?
Does clicking the pixels in the same place also gives opposite values in popup? Then there some issue with the process.
In case the values are same (and symbology is different), then
- remove the clipped layer, add the layer again.
- Execute the Clip tool again. Save the output raster in TIFF format (*.tif) in a basic folder (not inside a GDB).
- Restart ArcGIS Pro.
Think Location