Harris is rather different from Hitch or Dawkins in that his best skill is his ability to be precise with language. People just don't seem to know how to deal with that, because language is usually inherently vague. So he'll use a very specific corner case to talk about a very specific issue, and people will generalize his statement to apply in other cases where it wasn't intended.
One of the most obvious examples is the controversy caused by the statement "rape is perfectly natural", which was in one of his books. It was in the context of rebutting the naturalistic fallacy - the notion that if something is natural, it is somehow morally acceptable. His point was that something being "natural" tells you almost nothing about its moral content, and the example used was that many animals rape. This was then taken by some less than scrupulous critics and put into internet memes to suggest that Harris is pro-rape.
It's happened on a number of topics on issues that are hard to talk about because they're politically charged (nuclear deterrence and torture being two other biggies). Hence the following page, set up to clear up any such (often intentionally created) misunderstandings:
https://www.samharris.org/blog/item/...to-controversy