There absolutely are parts that will always mar the handlebars. The cheapest of brake levers have a three dimensional stamped body that has two edges contacting the bar. The scratches might have been caused by the shop trying to remove them, might have been caused during a previous adjustment, or might have been there from the moment the levers were originally installed on the bars.

The tech should make every effort to not scratch the bars, but there are scenarios where that is exceedingly difficult. Without having been there, I can only assume you were expecting them to make a silk wallet out of a sow's anus, and complained because it still smelled like a pig's ass.