SBT 0.13.xではスタックトレースが出力されるので、今質問は無関係になっている可能性があります。
jacek:~/sandbox/so/sbt-0.13.1
$ sbt run
[info] Loading global plugins from /Users/jacek/.sbt/0.13/plugins
[info] Loading project definition from /Users/jacek/sandbox/so/sbt-0.13.1/project
[info] Set current project to sbt-0-13-1 (in build file:/Users/jacek/sandbox/so/sbt-0.13.1/)
[info] Compiling 1 Scala source to /Users/jacek/sandbox/so/sbt-0.13.1/target/scala-2.10/classes...
[info] Running MyApp
[error] (run-main-0) java.lang.Exception: exception
java.lang.Exception: exception
at MyApp$delayedInit$body.apply(Hello.scala:2)
at scala.Function0$class.apply$mcV$sp(Function0.scala:40)
at scala.runtime.AbstractFunction0.apply$mcV$sp(AbstractFunction0.scala:12)
at scala.App$$anonfun$main$1.apply(App.scala:71)
at scala.App$$anonfun$main$1.apply(App.scala:71)
at scala.collection.immutable.List.foreach(List.scala:318)
at scala.collection.generic.TraversableForwarder$class.foreach(TraversableForwarder.scala:32)
at scala.App$class.main(App.scala:71)
at MyApp$.main(Hello.scala:1)
at MyApp.main(Hello.scala)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
[trace] Stack trace suppressed: run last compile:run for the full output.
java.lang.RuntimeException: Nonzero exit code: 1
at scala.sys.package$.error(package.scala:27)
[trace] Stack trace suppressed: run last compile:run for the full output.
[error] (compile:run) Nonzero exit code: 1
[error] Total time: 10 s, completed Jan 16, 2014 12:37:25 AM
私はそれが助けになるか分かりませんが、あなたのbuild.sbtに 'logLevel:= Level.Error'を追加しようとしましたか? –