It's really the second sentence that draws a long silence from Allison. Klaus was there and gone, so it makes sense that the two of them might have missed each other. But missing Vanya is a lot harder. Missing Vanya means forgetting the time that was spent here before Allison arrived.

"Vanya? Your sister. Number Seven?" Allison sits up more and tries to lean in closer to see if he's fucking with her. "You do remember Vanya, right? She was here with you for months before I got here."