Generally, exceptional is a compliment––"the concert was exceptional" means it was better than what could have been expected. But it can also just mean unusual. "Maria gets to skip gym, but hers is an exceptional case."
Exceptional begins with the Latin prefix ex- 'out,' because something exceptional stands out in some way. In certain cases, exceptional can mean under-performing. Children with special educational needs are sometimes referred to in this way, as exceptional or special.