Visual Inspections and permanent stains on equipment?

When performing visual inspections, there is alot of confusion to determine whether or not something is a permanent stain. My understanding is if you wipe it with a cleaning solution dampened cloth and nothing comes off onto the cloth and the stains remain, the equipment is visually clean. What if the stains start fading after each use, does that mean there is something coming off? Corrosion is a common problem I have seen in many facilities. Please give your input!

Has any analytic testing been performed to determine what “the stain” may be?

It could be corrosion or welding mark. Sometimes, welding on outside surface can cause black / copper red color stains on inside of the equipment, which will go off with time. So, your engineer can provide the best solution. Also, you need to look into your sampling method. you might have using a cleaning agent which cannot dissolve your stain (rust or oil based stain)