As you may be well aware, the shutdown.sh script provided in the bin directory of your Tomcat installation does not work. Tomcat docs even admit it doesn't work. But, they never fixed it for some reason. Below is short shutdown script I wrote that always works on Linux:

shutdown.sh

#!/bin/sh
TOMCAT_HOME=/usr/local/tomcat
pushd $TOMCAT_HOME
ps -ef | grep Bootstrap | grep -v grep | awk '{print $2}' > $TOMCAT_HOME/bin/tomcat.pid
export CATALINA_PID=$TOMCAT_HOME/bin/tomcat.pid
bin/shutdown.sh -force

You will have to set TOMCAT_HOME to your installation location.