Well, yeah, deployed a minified angular app yesterday, and ng-annotate handled almost everything except a controller that's initialized a custom way. So it broke. :(
That occasionally happens when you do things in non-standard ways, although ng-annotate has become quite smart lately and can now follow references and more. Did you use the latest version (also feel free to open an issue)? ng-strict-di in AngularJS 1.3 will greatly improve the error messages for these situations.
