i've noticed this a few times now. at some point, all refactoring tools simply stop working. they still suggest the correct action, like creating a property or implmenting a method, but selecting the action does nothing. the UI doesn't get broken or out of alignment, the IDE simply doesn't do anything at all. the issue fixes itself after restarting AppCode completely (project close/reopen doesn't solve it).
OS X 10.9, 10.10, AppCode 3.6.