I can answer when the Silence sabotage the TARDIS.
I don't remember which episode(s) it was. But some time before we knew what the Silence were, I think. There was some episode where Amy was in the TARDIS and was talking to the Doctor who was outside. She kept intermittently looking off-camera at something, and at one point even shouting "Hey!" at something off-camera. But then she carried on as if nothing had happened.
It's apparent now that was she was seeing was a Silence, but she kept forgetting about it as soon as he turned away. I'll look for the episode or the scenes, hope I can find it.
I agree that some of Moffat's stuff is too convoluted. But I still like his stuff and I liked RTD's stuff as well.
EDIT: Found it;
https://www.youtube.com/watch?v=A2E7KiFsKz8