3. Perception Filters
The thing about space and time in the Doctor Who universe is that its so easily manipulated. You cant ever take what you see for granted because you never know whos playing a trick on you. In Night Terrors (series 6) an alien manifests itself as a couples child so completely they dont even remember they were incapable of having children. There are clues no pictures of the mother while she was supposedly pregnant for example but they are ignored because the couple wanted a child so badly. Doctor Who often points out how easily we manage to fool ourselves when we really want to believe something despite all evidence to the contrary. So many times we are complicit in our manipulation. The Daleks in Asylum of the Daleks (series 7) use nanogenes (sub-atomic robots) to both physically and psychically manipulate their victims. When Amy is infected by them, her perceptions are so altered that she believes a group of Daleks are human. Since the Doctor is more aware of space and time, perhaps all the way to the quantum level, its much harder to fool him hes usually the one to point out theres something not right though it may take him a while to figure out exactly what the problem is.