I've found that they don't generally omit stuff, but the headlines and overall evaluations they give are suspect on more contentious items, almost to the point of a motte and bailey. So someone looking at the summaries will be mislead, but there's a more defensible opinion in the article proper.

Now, they do pull tricks like choosing which version of a claim to debunk and sometimes seemingly hunting for more obscure weak man versions of a claim than the more popular ones. Or they will "fact check" something that is clearly an opinion, like someone's read of someone else's motives.

The way I see it, though, they're hardly unique in this. Anyone skimming headlines is going to be badly mislead from nearly any source whatsoever.