But she'd also used those sneaking expeditions to spread the rumors about him trashing his reputation and causing their fellow students to look at him with suspicion and unease. Thereby, making sure the student body remained wary of him. Dumbledore didn't want Harry's naturally quiet and retiring personality swaying the children back to neutrality too soon. Neutrality that would quickly turn to adoration again because really speaking to snakes wasn't all that bad if no one got hurt by it. And so far no one had. Even the dimmest student knew that much. So she kept their mistrust alive with the careful spreading of rumors just as Ronald did with his wary attitude towards, and later lies about, Harry.
As for the supposed crime, well she hadn't done that, either. She'd been given the boomslag skin she'd needed for the advanced potion she'd decided they needed to make so they could find out more about the true Heir of Slytherin. And she was helped in the brewing of the actual potion because there was no way someone who had only been brewing potions for less than one calendar year could've brewed that very complicated potion at all. Let alone in a damp bathroom while still attending all their classes and trying to keep it a secret that they were doing so. Even the most talented beginner brewers would've messed it up. And good as she was at the time, she was only a beginner brewer.
Yet her brew had turned out perfect. Well, except for her supposedly using a cat hair instead of a human one. Which was only further proof that she didn't brew the potion at all. After all, if she could brew a complicated potion like the Polyjuice perfectly the first time she ever tried it, why then would she mistake a feline hair for a human one? Even Harry wouldn't have made that mistake.
Millicent Bulstrode's shoulder length hair was light brown, almost a dirty blonde, and very curly. Her cat was a short hair breed with a wiry, black coat of short, straight hairs. The cat was pure black without a hint of any other color. Even the shortest of Millicent's hairs would be a great deal longer, not to mention curlier, than her cat's. Because Millicent was female and almost no girls wore a buzz cut. Especially not in the wizarding world. So there was no way Hermione could've mistaken a hair from that cat for Ms. Bulstrode's hair. Yet she claimed she had. Even going so far as to allow him to see a black furred cat tail under the door of the bathroom stall she'd gone into for the transformation. A tail Ron had made certain Harry saw by silently pointing it out while snickering. Which meant Ron had been in on the deception though at the time he hadn't known that any more than he'd known Hermione was deceiving him.
Hindsight though was a wonderful and a cursed thing. Hindsight allowed Harry to see everything he'd missed at the time and to curse himself for his own ignorance. With the benefit of hindsight, Harry could see there were many things about that potion that didn't add up. Things, he hadn't given the attention they deserved because he was far too grateful to have someone claiming they believed in him and willing to hang around with him to see the smoothness of her claims couldn't be honest. Even as smart as she clearly was, she couldn't have been that far advanced in her reading to know everything she'd claimed to have known that year. Magic was too new to her for that. He'd spent the summer reading books about the magical world and what children his age raised in it went to school already knowing. Yet he knew he'd not only never heard of the Polyjuice Potion, he also knew there was no way he could've brewed it as she did. Not then. Nowadays he could and often had as it was one of the many potions he kept fresh and ready to use all the time. Being famous in that world and under observation in this one, there were often times when that potion came in very handy for him. But back then he hadn't even known it existed.
Now he knew he'd very neatly been set up. She and Ron had convinced him to provide a distraction in Potions so she could visit the Master's storeroom to get the ingredients they needed for the potion. He hadn't even questioned why she needed to access the Master's storeroom for the ingredients as both were available in the student storeroom. Nor had he thought to question how she planned to access Professor Snape's private stores which were locked against any and all students. Yet she'd clearly told him she had to get into his storeroom.