Both Jmockit and Jacoco instruments the class files. Jmockit does it first during the build process and when jacoco tries the same (later in the process) it says "oh oh, can't instrument an already instrumented class file". This issue happened with older versions of jacoco and jmockit. To see this error, enable --stacktrace option during Gradle build or --debug.
Now, using the latest jacoco and jmockit versions, we can solve this issue easily.
If you use jacoco (or use the latest one here):
toolVersion="0.7.1.201405082137"
or
toolVersion="0.7.2.201409121644"
or
toolVersion="0.7.5.201505241946"
See this: changes that went in 0.7.1 version.
For JMockit, you have to use jmockit version: 1.8 at least or later (1.9 to 1.13).
org.jmockit:jmockit:1.8
See this: changes that went under 1.8 version: http://jmockit.github.io/changes.html
I see the latest jmockit version out there is now 1.19, so use these two in Gradle with versions which are compatible and support each other.