Every flatpak app fails with this message:
$ flatpak run org.mozilla.firefox 
bwrap: Unexpected capabilities but not setuid, old file caps config?
error: ldconfig failed, exit status 256
Ubuntu Mantic, flatpak installed with apt.
It must be something with bubblewrap or with the way it’s used, because:
$ bwrap 
bwrap: Unexpected capabilities but not setuid, old file caps config?
$ sudo bwrap 
usage: bwrap [OPTIONS...] [--] COMMAND [ARGS...]
--help                       Print this help
--version                    Print version
...
More info for commenters:
$ type -a bwrap 
bwrap is /bin/bwrap
bwrap is /usr/bin/bwrap
bwrap is /bin/bwrap
$ ls -l /usr/bin/bwrap /bin/bwrap 
.rwxr-xr-x 72k root 28 Feb 10:38 /usr/bin/bwrap
.rwxr-xr-x 72k root 28 Feb 10:38 /bin/bwrap
$ sudo flatpak repair
[21/23] Verifying flathub:app/com.google.Chrome/x86_64/stable…
Checking remotes...
Pruning objects
Erasing .removed
$ unshare --map-root-user 
$ whoami
root
$ sysctl kernel.unprivileged_userns_clone
kernel.unprivileged_userns_clone = 1
I tried to set setuid for bwrap:
$ sudo chmod 4755 /usr/bin/bwrap
That makes flatpaks run, but with an ugly warning. I don’t think that’s a correct solution.

 
    