Any sufficiently advanced technology is indistinguishable from magic.
- Arthur C. Clarke
A plot hole isn't something that's not explained. It's something you can't explain.
- Steven Moffat
Where does she get the milk for the soufflés?
- The Doctor Asylum of the Daleks
Kill the Moon was a weak episode. The theme of whether one should be prepared to do evil in the pursuit of a perceived greater good is a favourite one with Doctor Who, explored famously in Genesis of the Daleks, and more recently in The Beast Below and The Day of The Doctor. The Doctor's motives for leaving Clara and Courtney to make the crucial decision could have been better explored - a line to the effect of "I trusted you to do the right thing. I didn't trust myself," would have made far more sense of his actions. But the big problem is that the premisses of the story just didn't make sense.
We have a pretty good idea what the Moon is made of and how it was formed. If it were the egg of a giant space creature, the Apollo astronauts would have noticed. Even if it were, it wouldn't suddenly become heavier when it hatched - conservation of mass is one of the most basic laws of physics, so if something gets heavier, the extra mass has to come from somewhere. Bacteria are the size they are because their simple prokaryotic metabolism won't scale up. An oversized spider has to be a multicellular, eukaryotic organism. Even if a giant dragon could hatch out of the Moon, it couldn't fly away by flapping its wings in space - wings need an atmosphere to work. And if it did fly away, the gravitational effects of such a large thing doing so would seriously perturb the Earth's orbit. And no organism could lay an egg larger than itself immediately after hatching.
OK, this is a show about an alien who travels through time in a ship that's bigger on the inside, but even in that context these errors break suspension of disbelief. There's a difference between asking, "What if time travel were possible?" and just not caring about basic physics. The Doctor Who production team needs someone to consult about the scientific plausibility of a story, someone who could tell writers when something didn't work, and what they could do to improve it. "Either you need another way to set up your ethical dilemma, or we can work out something else that could be wrong with the Moon."
The worst story this century could have been vastly improved by a bit of scientific advice. "The monster could be a giant intelligent slime mould that engulfs its prey, and absorbs their knowledge as it digests them. It adopts the likeness of previous victims as camouflage. After The Doctor notices that it avoids one particular woman, who wears a distinctive perfume, he realises that vanilla contains a hormone that will cause its component cells to disperse harmlessly."
Doctor Who did employ somebody in this capacity once. That was Dr. Kitt Pedlar, co-creator of the cybermen.
Even the most fantastical universe has to make sense.