Cross contamination between carbon steel and stainless steel, aluminum, or other families of nonferrous alloys can be a big problem if there is a concern with staining, corrosion, or cracking.
Stainless steel that has small particles of carbon steel (not carbon) on the surface will stain when they get wet. The carbon steel will rust and leave a stain that can be objectionable to the customer. The problem can be made worse if the stainless is in the form of pipe or tube and it is contaminated on the inside diameter or the outside diameter and subjected to a wet environment where there is an electrolyte containing chloride ions (seawater, brackish water, certain acids, etc.). The electrolyte will set the stage for galvanic action that can result in pitting, perforations, intergranular stress corrosion, and intergranular stress corrosion cracking. Again, the particulars of the environment and other issues have to be considered.
Copper contamination can also cause cracking problems. Copper can come from contact tips when using either FCAW or GMAW. Copper contamination can come from dragging a piece of copper pipe or tubing across a piece of carbon steel or stainless steel plate or pipe. Copper is not a preferred playmate with a host of base metals including aluminum, carbon or low alloy steels, and stainless steels to name a few.
I typically recommend that the base metals not be stored in the same storage rack. I recommend the steel racks have a non-metallic barrier between the base metals and the rack arms assuming the rack is constructed of carbon steel.
Grinding disks, flapper wheels, etc. should limited to use on one type of base metal. In other words a grinding disk that has been used on carbon steel should never be used on stainless steel or aluminum, etc.
Wire brushes used carbon steel should not be used on stainless or aluminum. Wire brushes used on anything other than carbon steel and low alloy steels should have stainless steel bristles and be used on one alloy family and not on other dissimilar alloy groups.
Stainless steel or aluminum components should be covered and protected if grinding is being performed on carbon steel in the same area. I prefer to see carbon steel separated from those work areas where stainless and aluminum are being worked on.
When working with alloys of titanium or zirconium, the issues mentioned become more problematic. Those materials should be welded in a separate room or shop from those working on carbon, low alloy, stainless steels, etc.
Does your boss have a right to be concerned? I would say, "Yes he does."
Best regards - Al