I think mostly from context or tone of voice only. for example, I can say 'ой, я все прослушала', which means 'oops, I missed everything somebody said'. so exclamation 'oops' obviously points to the fact that you failed to hear smth.
and when I say 'я прослушала лекцию/курс', in most cases it'll have the positive meaning, like 'I listened to/hear through a lecture/course'