I have the same problem on Incus virtual machines with my French azerty keyboard. The virtual machines are configured with the French keyboard (azerty) but the US keyboard (qwerty) remains active.
See this post : Linux Jails (containers/vms) with Incus - #276 by claude
I don’t have a solution either. It’s very embarrassing. Incus is not usable under these conditions.
I don’t have this problem with applications installed in Docker (ex: Nextcloud, Wordpress).