I am re-running a job from last year that combines colour pages and straight black pages. Last year the machine detected the black as black clicks but is not doing that now .... they are registering as colour. The content are tiffs and eps files. This issue has occurred in both Quark and InDesign documents.
I can't comment on Quark, no access to it, but Indesign sends color in BW by default, so that likely is controlling the color.
In both cases, Export to PDF and import the job to CWS and this won't happen.
From Indesign, the fix would be File > Print > Color Management and make sure it is not on "Let Indesign determine color"
From Reader File > Print > Advanced > Let Printer Determine Color
From Acrobat File > Print > Advanced > Color Management and make it None
If after doing that you still are getting click charges for color I would say there actually is color in them, all it takes is 3 pixels of color to get a click charge for color, if you believe that is not the case and have no doubt that the printer is at fault have Xerox send you an Analyst to verify it and they would surely refund the cost, but if the Analyst finds color in the job or an incorrect workflow causing the color click it would then make the issue File or workflow based and that Analyst visit would not be covered by contract.