Thanks for sharing this.
There might be this issue at play but there might also be something else at play.
just to be sure, where are located the classes in the target directory ?
I believe the sonar.java.binaries property should point to the output dir of SBT .class
So something like : sonar.java.binaries=target/scala-2.12/classes should get the compiled classes properly loaded and might help to solve your issue.