I have a sample Play 2.3.8 project that is composed by two subprojects (common and common2):
$ tree -L 2 .
.
├── build.sbt
├── common
│ ├── app
│ ├── bui
Indeed it seems that something changed between sbt 0.13.5 and 0.13.6. In my sample project I have all the subprojects defined in the main build.sbt, but had also them redefined inside the subprojects folder.
So in common/build.sbt for example, the subproject is defined again as
lazy val main = (project in file(".")).enablePlugins(PlayJava)
This works well in 0.13.5, but breaks after that.
So the solution was to remove those lines and only define the subprojects in the main build.sbt.