The opening scene shows Danny answering a phone-call from Clara. Yet when you see the screen on Clara's phone, it is showing that Danny is calling Clara. And to make it worse, it is the screen you get while the phone is ringing and you have the red and green buttons to accept or reject the call.
Dr Chang explains that the 'dark water' renders inorganic material invisible, however you can clearly see the chairs and the 'Activation' buttons in the tanks even underwater. You could argue that it's reasonable that the chairs are made of wood and covered with cotton, both organic materials, but this doesn't excuse the activation panels.
While on the phone with Danny, Clara's phone switches to an application thumbnail screen when she says, "Hey, Danny", and back to his face in the next shot.
In the opening scene of the episode, Clara calls Danny. Throughout the whole scene while the two of them are talking Clara's phone screen is showing a graphic as if Danny is the one calling her and she has to choose whether or not to accept the call.
Clara's gambit of throwing away the TARDIS keys to get the Doctor to do what she wants him wouldn't have worked. They are both well aware the Doctor can open his doors by snapping his fingers.