And here, we run into the other side of the problem with the automated takedown system as YouTube has it implemented currently: there's no human-in-the-loop confirmation step.
So at present: owner tags some content as owned by them, content is fingerprinted, YouTube does similarity-matching, content that is similar gets flagged for takedown until the uploader intervenes. It's certainly not fair to hold the content owner accountable for false-positives any more than it's fair to hold the uploader.
(Now, in cases where the uploader pushes the "This content is legit" button and the content owner responds with the "no it isn't" button, I'd be very much in favor of incentives changing so an error at that point on the part of the content owner gets them raked over the coals. But there's no real legal mechanism for that to happen right now. Remember, this entire process exists as an alternative to the content owner's legal option: to sue YouTube or to sue individual YouTube users. YouTube doesn't want that).