Maybe the photo does not represent the surface blemishes correctly, but it seems likely that some sort of inclusions became embedded on it. Does this make sense with the processes?
The surface has these small areas of black staining. Some thing is happening when the aluminium is in the ultrasonic wash?
Is there a chemical reaction taking place between the cleaning fluid and the aluminium . Fluid used is metanox.
Cleaning fluids should not cause any reaction. To understand what the stains are you would need a localized microscopic analysis performed by a knowledgeable and well equipped laboratory.