There are no shoes on the dirty floor, meaning Ayanami enters the room with her shoes on.
There is a mountain of mail even on the shoe rack. Shinji’s feet can be seen entering the apartment.
SHINJI:“Excuse me! This is Ikari… Ayanami! I’m coming in!”
Shinji is about to step up into the room with his shoes on when he stops.
thewayneiac: As you might have heard, the Japanese never go past the entranceway without removing their shoes. Shinji is more conciencious of Rei's home than she is herself.
