Note (1): Monero package is not yet verified on Flathub. In Whonix, as a security measure, only verified packages are allowed to be installed from Flathub when using Flatpak. Therefore, you won’t find Monero available for installation if you use flatpak in whonix by default.
To fix this you need to edit /etc/flatpak/remotes.d/flathub.flatpakrepo and change the Subset= from verified_floss to floss or to flathub (subset types can be found here)
So this will be kept happening until Monero fix their package on flathub.
Note (2): At the moment, Install monero package with flatpak using --user, not as system wide (without using --user), this is an issue of flatpak system side installation yet to be fixed inside whonix (need more relaxed restrictions) pointed here.