As both a Scala and Clojure user, I believe this is primarily a Scala-specific issue. The one caveat to that is that, if you're using Clojure and AOT-compile your code, you can run into some issues if you are trying to use AOT-compiled code from different versions (or using a different version of Clojure than the one used to AOT-compile the code).

Now, there have been some source-level incompatibilities, especially going from Clojure 1.2 to 1.3, and this seems to have been a bit of a headache within some parts of the Clojure community.