Theory:Doctor Who television discontinuity and plot holes/Dark Water


 * What is the point of hiding spare keys all over the TARDIS in the first place, if The Doctor looses a key whilst out and about what's the point of having spare keys all over the inside of the TARDIS, and why are they hidden in the first place who are they hidden from? If it's Clara clearly they are terrible hiding places and if to prevent other people from having them surely if they steal one of the keys then they're already in the TARDIS and if they are already in the TARDIS why would they try and steal a key that's only purpose is to get inside the TARDIS?
 * Perhaps they were hidden so that someone, say from U.N.I.T., were to be invited into the TARDIS, say to escape from something deadly, and took one of the keys. If someone from U.N.I.T. got a TARDIS key, they could get into the TARDIS whenever they find it, not just when the Doctor lets them in. As to why there are seven keys all in different places, I am not sure. He could be hiding them so that he can always have a key, and a companion (i.e. Clara) can't take them all. Clara was able to find them all, because either: 1. She had seen where the Doctor hid them, or 2. Because it was in a dream.
 * Since he does give them to companions at various times, it's good to have extras readily available. In addition, it does seem very much like the Doctor to simply leave them about in random places. As a side note, we also don't know if that really was all the copies that he had.


 * I know it was a dream but does Clara not realise that, even if she throws destroys all the keys, The Doctor can open the door with a click of his fingers? After all, she's seen him do it before and has even done it herself?
 * Clara was probably too stricken with grief with what happened to Danny. The Doctor knew this was a dream, hence why he didn't bother opening the doors with his fingers.
 * In fact, she LOCKED the doors. Finger-clickings or not, the door can't be unlocked without the key (I'm not even sure the TARDIS HERSELF could open her doors if they're locked, which is also the way I believe the "click of his fingers" thing works; the Doctor clicks his fingers and the TARDIS responds by opening her doors heself, not that the "click of fingers" is a pass-code or a controle switch or whatever. It's like if he knocked on the door and the TARDIS would open for him. But if the doors are locked, I don't even know if the TARDIS can open them HERSELF.).
 * In The Ghost Monument the TARDIS opens up for the Doctor after she lost the key, but it would make sense that Clara isn't aware this is possible.
 * In a dream state, we do not always think rationally. The Doctor let things play out, while Clara was simply not thinking properly, and so the finger snapping never occurred to her. It's also possible she is only aware of being able to snap her fingers to open and close the doors under certain circumstances. We've never seen her on screen open a locked TARDIS this way, only play with the doors while inside with the Doctor. She presumably isn't fully aware of how the mechanism works.


 * Why would The Doctor say "Go to hell," wouldn't it be more realistic for him to say "We go to hell?" If what he says is what he means than it makes no sense for him to say what he said.
 * Clara says: 'So, what now? What do we do now? You and me, what happens now? Doctor?' The Doctor simply gave a short answer for the second question, what do we do - go to hell, seems realistic enough.
 * Four Doctors imply that the Doctor was mad at Clara, and after he told her to go to Hell, he changed his mind and just improvised a reason for saying it.


 * If only organic matter can be seen through Dark Water, how can buttons and sentences 'Rest in Peace' be shown when the Cybermen push those buttons? Also how can the chairs be seen?
 * Who says those AREN'T made of organic matter?
 * In fact, the vast majority of buttons you see every day are organic matter—usually plastic or other synthetic organics, but still organic. How often do you see a metal or ceramic button, except as part of a retro 1920s design? And similarly for signage—other than glass tubes for neon signs, metal license plates, and fancy silicate or brass plates, most of the signs you see are on plastic or cardboard or something else organic.


 * If the skeletons in the mausoleum were actually Cybermen, and looked like skeletons because of the dark water, then why was the noise they made when they turned their heads sound like cracking, rather than something mechanical?
 * It's possible that was an "added effect", much like the incidental music that plays during the programme (which is obviously not heard by the characters). Alternatively, the sound may have been altered because they were immersed in fluid.


 * If the skeletons in the mausoleum were actually Cybermen, and looked like skeletons because of the dark water, then why was it clearly shown that the skeletons touched the button and the glass.
 * Refraction of light in water often makes things look like they're in different places than they really are, and also we must keep in mind that this is a liquid that we are completely unfamiliar with, and we do not know the properties of this liquid so we don't know how light interacts with it.