I have tons of “unconnected” on a circuit I have made previously, and even realized and it works as designed.
But since KiCAD 6.0.0, its DRC is detecting tons of fake unconnected. I couldn’t understand where they are coming from (I discovered it later. See below)
This is not an answer to your question, but you don’t have to delete those manually. Under “clean up tracks and vias” there is a setting to delete all tracks which are completely within pads.