BMitch is right.  Docker has nothing to do with runlevels, it will never change a runlevel.  But there is more.
runlevel unknown is common on some systems running systemd.  Your question is tagged with Debian though, and Debian Jessie (the latest Debian release, which uses systemd, uses compatibility script to print a runlevel).  Arch based distros, and the unstable RedHat based distros (e.g. Fedora) print unknown when executing runlevel, i.e. they do not even care to print a fake runlevel.
If you check your runlevel script you will get the following output on a recent distro:
$ ls -l $(which runlevel)
lrwxrwxrwx 1 root root 9 Jun 18 14:44 /usr/bin/runlevel -> systemctl
(that is on arch, runlevel is in /usr/sbin on Debian, but it also points to systemctl on Debian)
The runlevel script points to sysemtd control on most recent distros.
In general runlevel has no meaning on recent distros (because of systemd to which pretty much everyone switched to).  If you look inside the /etc/rc.d/rc*.d/ directories, they're almost empty.
What is actually defining how init processes the system boot is the systemd default target, located here:
/lib/systemd/system/default.target
Or /etc/systemd/system/default.target, if that exists.