In the episode, Father's Day reapers appear due to Rose causing a paradox. "The Doctor walks back to the TARDIS, he senses that something is wrong. When he gets back to the TARDIS and unlocks it with his key, he finds it an empty box." Later in the episode it somewhat touched on the reason, however, I still don't understand.
As SpaceWolf1701 says it is probably a bit timey-wimey, but as explained in the episode, the reapers are creatures of time that live inside the time vortex, hence it is probably not too unreasonable to assume they removed the interior dimension of the Tardis to prevent anyone escaping, allowing them to feed off the paradox for longer.