When we don't use pid namespace or use pid namespace with path in config.json, we can reproduce it by steps:
[root@localhost systemdtest]# runc --systemd-cgroup run -d test
[root@localhost systemdtest]# runc --systemd-cgroup exec -d test sleep 2000000
[root@localhost systemdtest]# cat /sys/fs/cgroup/system.slice/runc-test.scope/cgroup.procs
278991
279011
[root@localhost systemdtest]# runc --systemd-cgroup delete -f test
ERRO[0000] remove /sys/fs/cgroup/system.slice/runc-test.scope: device or resource busy