From the way he spoke to her, it sounded to Haibara like this boy might be used to dealing with children. Still, that might only make things worse for her... at least in this situation.

"Not really," she says, "I shouldn't have been running. I heard our rooms have bunk beds, and I wanted to claim a bottom bunk before somebody else got there." The lies came easily. It was a reason to run in that direction (at least for a kid) that wouldn't lead him to trying to help or investigate. That would be an unideal situation.

If what she heard was true, the door to the room she was staying would be adorned with the name Shiho Miyano, and that would cause too many questions. Even if she had to slow down a bit here to cast off suspicion, that'd be the better choice.