I noticed this problem with Tomcat6 in FC10 and FC12.
When tomcat started in debug mode JAVA_OPTS contains a dt_socket definition.
Since tomcat shutdown script uses JAVA_OPTS, stopping tomcat fails.
I don't know if JAVA_OPTS is needed at all when stopping tomcat, but if it is needed, I patched /usr/sbin/tomcat6 stop function to delete the debug info from JAVA_OPTS.
It is as follows:
< # Fails when JVM debug defined - patched by dTb
< JAVA_OPTS=`echo $JAVA_OPTS | sed -e 's/\(.*\)-Xdebug -\(\([^ ]* \)\|\(.*\)\)\(.*\)/\1\5/'`
It may not be be the best solution and it works for '-Xdebug ...' definition only, and not for '-agentlib ...' definiton, but it might be a good starting point to solve the problem.
Balazs D Toth