Hey Daron,
This is because the macOS' permissions settings are buggy.
If you need to find the Keyboard Maestro Engine, here's the simplest way:
Finding the Keyboard Maestro Engine in the Finder
@peternlewis – it really seems like a good idea to add Reveal Keyboard Maestro Engine.app to the Keyboard Maestro Editor's Help menu.
This issue keeps coming up over and over again.
-Chris