See this answer. It seems that MySQL driver should be in {$TOMCAT]/lib
shared between applications. Check that you are not including it with each application. At least it worked for me and I have been able to remove the warning.
If you are using Maven mark the dependency as provided.
UPDATE:
root cause is that Tomcat have problems to garbage collect the driver because it is registered in a singleton common to several applications. Closing one application does not allow Tomcat to release the driver. See this answer.