From the Help menu go to the AlphaCocoa Web page, which opens in a help-viewer window inside Alpha. Now navigate to a page with a search field, write something and press return. The return is not cpatured by the search field or the help-viewer window, but passes instead through to the topmost editing window in Alpha.
Several other key combinations go through to editing windows, such as ctrl-s.
This is fixed now. Installed a class method ignoreBindingForKeyCode and delegate methods windowDidBecomeKey and windowDidResignKey in class AlphaRoot.
Will be in 9.0b1.