I have a Tomcat 7 running in Linux that I start via $CATALINA_HOME/bin/startup.sh and shutdown via $CATALINA_HOME/bin/shutdown.sh
Tomcat 7
$CATALINA_HOME/bin/startup.sh
$CATALINA_HOME/bin/shutdown.sh
Check if your Web Application has some Scheduler active, like Quartz.
If you don't stop it, Web Application Thread never ending until you kill it