One issue that I ran into when generating JaCoCo reports is that I would get different reports for each of my test tasks. What I needed was to join the reports and get a single report for the overall test coverage of my code.
Gradle
JaCoCo is one the most used tools for generating coverage reports for JUnit tests. One of the reasons for it being so used is it's seamless integration with tools like Jenkins, SonarQube, Maven and Gradle.
With Gradle, very little comes out of the box and a lot of the filtering and configuration you need to do on your own. That can be confusing at first especially as a beginner and even more so if you are accustomed to Maven.