Theory:Doctor Who television discontinuity and plot holes/In the Forest of the Night


 * The Doctor's theory and supposition that the trees don't burn due them collectively acting to withhold Oxygen is dubious at best. Trees don't consume oxygen, they produce it. Simply arranging for the trees in a given area to not produce oxygen once a fire is lit would not extinguish the fire, as there is still oxygen already present. Failing to add more wouldn't extinguish it. Think fires in office buildings, apartment complexes and the like. No trees around to continually produce oxygen, yet fires still burn.
 * Just like most of the living things, trees consume oxygen and produce carbon dioxide. They just SEEM to produce oxygen because they produce oxygen by photosynthesis and quantity of produced oxygen is greater than consumed oxygen. If trees can somehow control their photosynthesis and respiration (as the Doctor suggested), they would rapidly consume oxygen and emit carbon dioxide, extinguishing fire. (Of course, this doesn't make sense in real life, but in whoniverse...who knows?)


 * Once they realize what they are up against and the disaster that has befallen them, Clara says "If you can't save them all, save who you can. The Tardis. It's a lifeboat, isn't it? Not everybody has to die." They make their way back to the Tardis, and inexplicably Clara says that the Doctor has to leave without the kids, and without her and Danny. Who exactly was she anticipating that the TARDIS would be a lifeboat for?
 * The Doctor. Clara believed that the kids should be with their families at the end, and she and Danny would bring them home since Clara didn't want to leave Danny behind. She had hoped she could convince the Doctor to save himself.