This only happens when shell expansion is used in tomcat.conf.

To reproduce:

1) Add some shell expansion to tomcat*.conf

$ echo "JAVA_OPTS=\"${JAVA_OPTS} -Xms1m\"" >> /etc/tomcat/tomcat.conf

2) Start tomcat and verify that there's only one instance of the Xms argument

$ service tomcat8 start
$ ps aux | grep tomcat | grep -o \\-Xms1m
-Xms1m

3) Restart tomcat to duplicate the JAVA_OPTS

$ service tomcat8 restart

4) Verify that there are multiple Xms args with ps

$ ps aux | grep tomcat | grep -o \\-Xms1m
-Xms1m
-Xms1m

This is because when using restart the stop and start are called in the same script and the parseOptions reads the configuration files twice instead of once to just start/stop the service.