It was the evidence that damned Apple to begin with. Evidence their lawyers fought to have dismissed before the trial even came.
Just keep in mind this isn't like a criminal case, where all evidence is presented and debated in front of a (hopefully) impartial jury. It's a bench trial. The judge gets the evidence handed to them, looks it over, makes a decision to move forward based on what they've seen, then has the defendants come in and explain the evidence in a different light. If the judge is impressed by the explanation, they're innocent. If not, they're guilty.
Yeah, it does sound like you're being deemed guilty before proven innocent, but this is the way all antitrust cases are held. A corporation isn't pulled into court unless there's enough damning evidence to justify it.
If Apple thinks they were treated unfairly, or the evidence interpreted wrongly, they have every right to an appeal.