xinput only deals with X11.
Wayland can use Xwayland to run X11 software, but they live in their own little X11 world. You probably have some Wayland-native programs and some X11 programs running
you can list running X11 software with $ xlsclients.
There are a couple suggestions there to remap things. I haven't used input-remapper myself, but I've heard positive things about it. It's packaged in Debian trixie.