I have the same problem using Grails/Groovy/Gradle. As I understand, configuring Java to use JaCoCo agent making instrumentation at runtime, so you don't need to include dependencies in your built (pom.xml).

Check the content of your jacoco.exec file (I assume it is not empty). For that run command: java -jar <jacoccli.jar-path> execinfo <jacoco.exec-path>. This will list all classes, for which JaCoCo collected coverage info. In my case there are only from apache package. So it checks the coverage of the small part of the Tomcat itself and not webapp, it is running.