Plugging screw holes? Use plated fasteners. Unplated steel is the most common woodscrew you’ll encounter. Most of these carry some type of oil or a waxy dry lube, but this is a just minimal barrier meant to prevent rusting until the screw is used. This is usually fine in most projects that will reside in heated/air conditioned spaces.
When plugging a fastener hole, extractives in the wood can cause the fastener to begin to rust and cause a dark staining around the plug. Plated fasteners, such as clear or yellow zinc, prevent staining by creating a sacrificial zinc barrier over the iron. So if, you are plugging, remember the plating.