I am using intellij 14 with scala 2.11.6 installed using home brew and symlink using
ln -s /usr/local/Cellar/scala/2.11.6/libexec/src /usr/local/Cellar/scala/2.1
2019 update... I'm running Ubuntu Linux and IntelliJ community 2019.1 with sbt 2.13.1 and got the exact same error. I also found that if I built directly from sbt with "runMain package.MyClass" it worked, so I knew it must be an IntelliJ problem, not a "real" problem.
Anyway, I found the file .idea/libraries/sbt.. lots of crazy long name ... scala_library_2_13_1_jar.xml.
In it, there was an XML block , and in that block, two entries were duplicated: I first noticed the scala-library one, and after deleting that, the error report came up about the scala-compiler duplicate too. After deleting both duplicates, my build is now working.