After running flatpak run org.geany.Geany, switching to a git folder and running 'git pull' in the intergrated terminal I get the same error message:
Bad owner or permissions on /etc/ssh/ssh_config.d/50-redhat.conf fatal: Could not read from remote repository.
Why it is looking in that folder and file for authentication, which do exist, i.e. 50-redhat.conf, I don't know.