In previous episodes featuring the Silents, we'd often see the interaction with them before the character turned away and forgot about it. This time around, we see mounting evidence between cuts that they have been dealing with them repeatedly during a single scene (the Doctor's rapidly increasing tally marks, Churchill and the Doctor both suddenly having weapons in their hands, etc.) Does that mean the scene was filmed so that the Silents just never appeared until the end of it, or were their appearances filmed and the audience just forgot?
Unintentionally Unsympathetic: River Song, as seen above. She's clearly meant to come off as a Woobie, Destroyer of Worlds, but the fact that her actions threatened every single thing in the universe (including her parents, who were right there with her), along with River not even so much as flinching when this is pointed out to her, caused many fans to completely brush her off.
What Do You Mean, It Wasn't Made on Drugs?: The opening scene before the credits has dinosaurs in a public park, flying car balloons, classical authors on a talk show, the Holy Roman Emperor in 21st century Britain with the emperor himself being Winston Churchill who has a Silurian for a doctor. What the hell is going on?