She could have taken a shower while he was going to sleep. We don't know what happened during the intermission. However the MC is an idiot for interfering in her "fun time" in the alley in the first place. Once he found out it wasn't rape he should have just let her be. Then again we know MC is an idiot.
She told him that she was getting railed by two random dudes in an alley by choice yet he thought he was helping her. He believed her lie about not having a home to go to although she works at the same place as his sister and paid for food at a restaurant that has a private room. Not only that, but she specifically told his sister to take a hike when she ran into them at the restaurant. He should have been able to clue into the fact that she was on the prowl at that point.