Yes, he did disavow Duke, in 2000 when the Reform Party nomination was in play. What happened, old age?
But that unfairness is a very real thing that Trump is going to have to handle better if he wants to win the general election. Between the media and the Dems, Republicans will be held to a higher standard, and so the GOP nominee must meet that standard.
It's one of the problems in nomination a non-politician, because they're simply not used to speaking in a way where every word is measured. Trump has broken that mold in the primary, but I'm not sure that will work in a general election.