Rudy's toilet habits... he may well have flushed and not checked to make sure his deposit had disappeared. Perhaps he didn't know about the faeces until he read about it in the press?
I find it more likely that he was interrupted before flushing, such as in this scenario:
A little before 9 PM, Rudy enters the driveway to the cottage. He knows the boys downstairs are out of town and the upstairs looks empty. The girls are away for the weekend or at least out on the town. In previous visits to the cottage, he noticed the problem with the upstairs window shutter. The streetlight shines on the other side of the cottage and it's more open to the road. This side is more sheltered, the trees in the driveway block the view. Using a stick, Rudy moves the green exterior shutter out of the way and lobs a large rock through the window. He waits in the shadows for a while to see if the rock woke anyone up, but the cottage remains quiet. Climbing the up the bars on the window below, he reaches in the broken window, flips the latch and pushes the window open. There is still some glass on the sill, but his gloves and clothing protect him as he lifts himself up through the window. This isn't the first time he has entered a building this way. Once inside, Rudy pulls the shutter closed and turns on the light. He feels pretty safe now that he is inside. The girls shouldn't be showing up anytime soon. Rudy is looking for cash so he can pay the rent due on Monday. He notices a laptop he might grab later, but needs his hands free for now. No sense lugging it from room to room.
Rudy's stomach has been acting up tonight, so he takes a break from burglary. He drinks some juice he finds in the refrigerator and heads to the bathroom. Just as he is finishing up, the front door to the cottage is opened. Rudy reaches into his pocket and takes out a knife.