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
I had the same issue than you experimented and the solution, actually very easy, was actually erasing the .idea folder from the project, the problem is that the configuration inside of this folder (containing the set ups for example for the test, VCS, the runs, etc) gets corrupted with double entries (probably cos you update your Scala version), once you do this and reopen the project in Intellij the IDEA will generate a fresh new configuration for you.
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.
Maybe you have used
/usr/local/Cellar/scala/2.11.6/
as the path for Scala SDK?
When you install scala with homebrew that path will contain not only the scala libraries, but also a symlink with the relevant libraries for intellij. So if you use the top-level install directory intellij will find the libraries twice.
Instead you should use
/usr/local/Cellar/scala/2.11.6/idea/lib
Remove the following line in build.sbt:
...
scalaVersion := "2.13.0"
...
Try rebuilding and running it again
Delete multiple versions of scala-library in sbt, leaving one.
To fix the problem go to project structure in intellij and go to global libraries It should be like this
After that remove all the scala SDKs by hitting the - mark
Next, click the + and choose your Scala SDK version to add
After that please make sure to apply the changes and re-run the program