public class EstadoActual extends Fragment {

    // this controls work perfect
    @InjectView(R.id.txtWork1) AutoCompleteTextView txtWork1;
    @InjectView(R.id.txtWork2) EditText txtWork2;

    // this controls are inside the viewstub,
    @InjectView(R.id.viewstub) ViewStub viewStub;

      MyDynamicView  myDynamicView;
.. .. ...
    // class (inner in this example) that has stuff from your stub
    public class MyDynamicView {
      @InjectView(R.id.txtDontWork1) EditText txtDontWork1;
      @InjectView(R.id.txtDontWork1) EditText txtDontWork2;
       public MyDynamicView(View view) {
         Butterknife.inject(this, view);
       }
    }

   @Override
    public View onCreateView(LayoutInflater inflater, ViewGroup container, Bundle savedInstanceState) {
        View rootView = inflater.inflate(R.layout.festadoactual, container, false);
        ButterKnife.inject(this, rootView);
      ... ..
        View viewFromStub = viewStub.inflate();
        myDynamicView = new MyDynamicView(viewFromStub); // this is the main point where you configure your view
        Fill();
        return rootView;
    }

   private void Fill(){
        txtWork1.setText("Hello 1");
       txtWork2.setText("Hello 2");

        myDynamicView.txtDontWork1.setText("Don't Work 1"); // This should work for you now
        myDynamicView.txtDontWork2.setText("Don't Work 2");
    }