Darwin was 'wrong' about the tree of life because he didn't have the picture we have today. In that article it says of Darwin's tree, "The tree of life is not something that exists in nature, it's a way that humans classify nature." Well, yeah, and Darwin himself said pretty much the same thing, "The affinities of all the beings of the same class have sometimes been represented by a great tree. I believe this simile largely speaks the truth..."
He thought it was a good analogy, and it was. Now that we know more, his tree is simplistic. He had no idea that branches from his tree could be cut, and grafted onto other branches. That requires an in-depth understanding of biochemistry that he couldn't possibly have jumped to.
It's not so much that Darwin was wrong. He was right, he just wasn't privy to the finer details we now have, in large part thanks to folks like himself.
But, just putting the word Darwin and wrong in the same sentence is enough to whip up a frenzy of quote mining and rhetoric that lacks context. That is where I think basic science education is doing poorly.