… the fun in rewatching season five will be finding all those weird instances that might have seemed like production errors but were actually references to The Silence (similar to the dilemma involving the Doctor’s jacket in “Flesh and Stone” last year). There are two instances in “The Lodger” specifically, where we might have Silence sightings.
Around the episode’s fourteen minute mark, the Doctor is talking Amy through stabilizing the TARDIS (remember, she’d been trapped onboard when the TARDIS inexplicably started moving around). As the Doctor helps Amy get the blue box into a calmer mode, he tells Amy that he’s got more work to do. Their conversation ends with Amy looking slightly to the right of the camera confusedly, and shouting “Hey!”I don’t know about you, but that’s not how I end conversations, even with centuries-old aliens.
Then around minute twenty-two, Amy simply stops paying attention to the Doctor’s phone conversation, staggers back, and gasps. “Hey!” she shouts, “Hang on!” Then she blinks, and everything’s back to normal.