https://www.quantamagazine.org/neutral-theory-of-evolution-challenged-by-evidence-for-dna-selection-20181108/ The article above challenges how mutations work in evolution. Does this disprove the theory of evolution?
First, please note that the article you link is not a peer reviewed article. It is a popular, easy-to-read article.
Does this article call into question the theory of evolution?
No, it does not. What makes you think it does?
The article talks about a very old (and somewhat still ongoing) debate about the relative importance of genetic drift vs selection in evolution. I suppose that you may have portrayed selection as being the only evolutionary process and I suppose that reading about genetic drift as being another evolutionary process may have make you feel like "we were wrong all along" while in truth we have always known a bout it. Note that even Darwin with his very limited understanding of evolutionary processes (compared to what we know today) knew that there are other evolutionary processes than selection.
You might want to read about genetic drift. As a start you could read the following: