Thank you for reporting this bug. We will make it our priority to review this report.
different behavior between sencha-touch-debug.js and sencha-touch-all-debug.js
By using sencha-touch-all-debug.js when I set refs and trying to use getter this.getRef () when the ref has not yet been instantiated is returning undefined.
When I change the app to file sencha-touch-debug.js works properly as it should (if the instance is returned if there instantiates and returns).
I believe that the information is sufficient, if you need details I am available.
I just tried a test and it is working for me. I instantiate a class, in the controller I use the getter created for the ref and it always returns the instance.
This in 2.1.0