Is your terminal SBT and your Emacs (or Spacemacs) SBT giving you different results? More confusingly, is SBT doing the correct thing from inside Emacs if Emacs is started from the terminal and not as a GUI application?

This can be caused by Emacs producing its own environment if started as a GUI application! (And you thought all environments were created equal, out of .bashrc or whatever … Nope.)

This new env that Emacs creates for itself is based on … magic, I guess.

In any case, it does not necessarily respect the JAVA_HOME that you carefully set in your normal (terminal) environment.

In order to correct this, add to your init.el (or dotspacemacs/user-init in .spacemacs):

(setenv "JAVA_HOME"
        "/Library/Java/JavaVirtualMachines/jdk1.8.0_172.jdk/Contents/Home/")

or whatever it is that JAVA_HOME should point to.

As an alternative, you can set this variable per project by adding a file .sbtopts in the project root with the following:

-java-home /Library/Java/JavaVirtualMachines/jdk1.8.0_172.jdk/Contents/Home/