During the frame/pre sheetrock phase inspections on new homes I commonly see this condition "shiners". These are nails that have missed the riser/joist and have been left in. These nails should be removed so that squeaky stairs and second floor subfloors do not squeak when walked on in the future. I always ask the builder in the report to fix this condition. It's an easy fix at this stage to prevent an annoying problem in the future. It's more complicated to fix after the sheetrock and flooring is installed.