Kaito wasn't a normal boy. Aoko had figured this out almost as soon as she met him – he was smarter, and nicer, and could do magic. He stayed not-normal as they grew up; even if he did some of the same things as other boys, he did them differently. And he was always her best friend.
In their second year of high school though, Aoko started to notice a few things about him, things that were even more different from normal boys. It wasn't the make-up – he'd been doing that since they were twelve, and she'd gotten used to the smell around him – or even his fastidiousness (he'd always taken a little more care than most boys, although that had increased, she thought, but she wasn't sure). It was the way he was quiet sometimes, or occasionally had bandages in odd places, even though she knew there was no way he could have gotten them. The way she sometimes thought she saw him thinking deeply before he noticed, and became her smiling Kaito again.
It had been suggested – implied, really – by certain people (notably their classmate Hakuba) that Kaito might have been the Kaitou Kid. The very thought horrified Aoko; there was no way it could be possible. She herself had provided him with an alibi after all. Even if he had changed since Kid had reappeared.