kicadiff check ran kicad-cli DRC against whatever zone fill was saved in the file, so a zone edited and saved without refilling, or a script-generated board, reports every pad the pour should connect as unconnected, which the designer never sees in the GUI. Checking a board against itself reported changes and exited 1. The --refill-zones fix only exists in KiCad 10, so KiCad 9 users get a warning instead.