Keep in mind that not every fight in game accurately represents how the lore is supposed to have gone down. Malygos was taken down by a team of adventurers. Yes, he was powerful, but he was also highly screwed up in the head at the time. I would gather that the overall impression is supposed to be that he was somewhat weakened from having the Reds constantly in his face for some time as well.
Kel'thuzad? If that's who you meant. He was gifted for a lich, but a lich is still just an resurrected mage and they are not all powerful by themselves.
Those are just my interpretations though. Blizzard has been known to make mistakes and often doesn't fully flesh out the lore of the lesser villains. I'd certainly say that Malygos is an example of that as they were so focused on Arthas for the whole expansion, that other parts didn't really get the treatment they deserved.