It’s not a problem at all, it’s just a script that is perhaps a little too verbose.
Karaf is the application container that openHAB uses, it allows you to talk to the openHAB server with SSH and the like. KARAF_HOME is set to /usr/share/openhab2/runtime/ in a startup script. I assume it’s ignored because the stop command is called from the KARAF_HOME directory anyway, making it irrelevant.