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