The Doctor was a quintessential bachelor, cleaning up after himself? Completely not a priority. Even with the new companions to be traveling with them. The ship didn't look that bad.
"That's the one thing I do miss about Mickey," he thought aloud, still unmoving from his spot on the couch, "Always did the dishes." Perhaps only because the Doctor had told him they all had chores (chores! pssh!), and his was dishes. What was the Doctor's? Washing the car. The boy could not be the brightest color in the box sometimes.