It's understandable why they do that, but it can put journalists/writers of articles with clickbaity headlines in a tough spot, as they are often forced to defend headlines they never wrote in the first place!
Tell me about it :-) I do the headlines for pieces I write and obviously no one's going to change them on my own blog. But I do write for other venues as well--and I admit I'm not the world's snappiest headline writer--and they do sometimes get changed to things that don't quite match the content of the article.
However, to be fair, headline writers have been writing "clickbait" headlines for far longer than there have been clicks. Headlines in magazines and newspapers have never been scientific journal titles.