Stains on your a medical instrument can be removed, but rust can leave damage forever.
So how do you know if a brownish-orange color is rust or a stain, use the eraser test.
Use the eraser and rub it back and forth until the discoloration has been removed and the surface underneath is smooth and clean, then that means it's a stain.
However, if a pit mark shows up on the metal after the discoloration has been removed, then this is corrosion, which will continually rust.
Troubleshooting Stain Guide:

• Orange/Brown Stains - Most individuals think that when they notice orange/brown stains that it is rust.
  When this stain color appears as a result of PH surface deposits, it is a result of any of the following: Chlorhexidine usage, improper soaps and detergents, cold sterilization solution, possibly baked-on blood, soaking in saline or using laundry soap.
  
• Black-ish Brown Stains - Low PH (less than 6) acid stain.
  It may be caused by dried blood and/or improper soaps and detergents.
  
• Blackish-Blue Stains - Reverse planting may happen when different metals are ultrasonically processed together.
  For example, when you have stainless steel surgical instrument sets precede with chrome surgical instruments will cause a stain color reaction.
  This blueish black stain will occur if blood, saline or potassium chloride will make this bluish black stain appear.
  
• All-in-one color stains - Excessive heat by a localized "hot spot" in the processing cycle.
  
• Dark and Light Spots - When you allow forceps to air-dry.
  With slow evaporation, the minerals (sodium, calcium and magnesium) are left on the medical instrument's surface.
  
• Bluish Gray Stains - This happens whenever cold sterilization is being used outside a manufactuer guidelines.
  
• Black Stains - Whenever amonia is present.