I have been in a similar situation, but on the other side. My own MS thesis and an article derived from it contained a major flaw. In short, the thesis was about investigating some static waves in a certain system, but the system itself is unstable in the very same model, with the instability length being comparable to the characteristic wavelength of the static waves in question. The whole investigation did not make any scientific sense at all, because the assumed system could not be physically realized in the first place.
I myself discovered the flaw a few months before submitting my thesis. I discovered the flaw pretty accidentally: I wanted to formally prove that the system is stable, but the result of my calculations showed that the opposite is true. I had never heard from my supervisor, who had given me the problem for my thesis, or from his colleagues that the system may be unstable. Everyone simply did not even think about that possibility.
And then I faced the dilemma as to what to do.
My final choice was to tell no one and to simply get my degree. I was an undergraduate student graduating from a Russian university, and getting my MS degree asap and moving abroad to get a Western PhD degree was my highest priority. If I had raised the issue about the flaw, I would have suffered a major setback in my career. I would have had to start my MS project over, and I am not even sure whether I would have been allowed to do it at all. If I had had a setback in my career, I would not have been able to win a prestigious PhD stipend in a Western country.
I should have checked at the very beginning of my MS project whether the system is stable. I should have, but I did not. Partially it is a fault of my supervisor, who directed my work in a very rigid way, giving me concrete tasks and deadlines. He never told me to check whether the system is stable. The official research plan, which I and he signed, did not contain any mention of a stability analysis. It was my own initiative to try to prove stability, because I felt that this was needed to make my investigation complete. I did not even talk to my supervisor about my idea to perform a stability analysis. After I discovered the flaw, I was sure that if I talked to my supervisor about the flaw, he would say the whole MS project had to be canceled.
After I submitted my thesis, my supervisor insisted that I write and publish an article derived from the thesis. I did not want to do it, but I had to. After all, I needed good recommendation letters from my supervisor, so I had to obey. The article was published in a reputable American journal and was cited ~20 times. Writing that article was the most unpleasant experience in my scientific career.
No one noticed the flaw, so I successfully got my MS degree in Russia, moved abroad, got a Western PhD degree, and some years later published an article explaining the flaw. I explicitly wrote in that article that my previous article and a number of other articles, which I cited, are invalid science. No one published a comment in response. In private conversations, my colleagues confirmed that my conclusion about the flaw is correct.
Why did I wait about six years to tell the scientific community about the flaw? Don't hate the player, hate the game. I simply could not afford a career setback. I needed my MS degree asap. I believe I made a wise choice. I would do exactly the same in the same circumstances. Who wouldn't?
Concerning your question, the principal thing is this: what's in it for you? Does the guy's article make any harm to you or your reputation by, e.g., contradicting your own articles? If it does not, then I want to tell this: there are so many wrong or misleading articles in science, there are so many awful things in science, and the guy's article is a drop in the ocean of all this. Why wouldn't you focus on doing your own great research instead? I guess the guy's article is insignificant anyway and is not even worth considering, just like most articles in science. I guess it is just a mathematical or computational exercise made for the purpose of producing a paper and earning a PhD degree. If my guess is correct, then you do not need to stoop to that level and search for mistakes in insignificant articles, and you do not need to harm the guy's career at its very beginning. I have articles published in Physical Review Letters, even as the first author, but I started my career with a wrong and misleading MS thesis.
Imagine you noticed a mistake in an article published in Indian Journal of Physics, whose impact factor is below 1. Would you care to correct the mistake by publishing a comment? I doubt you would. Not every mistake must be corrected. Some are just not worth spending time and effort correcting them.
My own principles are simple:
All physics journals that are "lower" than Physical Review journals are trash bins.
If an article does not interfere with my own research, then this article is none of my business.
I hope that my post will help you and others look at the issue from an angle different from the one from which many people see the issue.