Do you take any particular precaution when you trim your part with your Dremel ? How do you protect the surface from scratches that may occur during the trimming ?

I don't suspect the pump itself, but for being 100% sure, how can perform such a test ?

Yea, the bubbles are there because they are pinholes on the carbon, behind the gelcoat. If you look closely at the part, you'll see those "bubbles" are in the intersections of the tows, typically where pinholes form. Remember the gelcoat is hard before you infuse, so the pinholes are the same ones you had on the first part, they are just covered, which makes them bubbles, if that makes sense.