What should I do if actually I found a serious flaw in someone's PhD thesis and an article derived from that PhD thesis? Recently, I came across a PhD thesis and an article derived from that PhD thesis and found a serious flaw in them that actually makes their conclusions invalid.

In the first place, I was unsure if I'm right or not, so I contacted the guy that wrote the PhD thesis and subsequent article and described my concerns and I showed my calculations to him and asked if he thinks in fact there is a major problem in his PhD thesis and that article, which is derived from it. He responded back that embarrassingly, in fact I'm right and there is a problem but he can't do anything about it.

I didn't want to force him to do something but I'm just thinking maybe there might be a possibility to publish an erratum for at least that article. It's a major flaw and unfortunately it just invalidates the major conclusions of paper and PhD thesis. Surprisingly, the article is cited for 15 times and nobody found that obvious problem. My question: What's the best way to deal with these kind of situations that even author himself/herself admits that in fact there is a major flaw in his/her thesis or article?
One possibility is for you to write a paper on your reanalysis. Often this would need to be something more than pointing out the flaw alone, but that may be discipline-dependent. If the flaw you have detected is a key part in your own analysis of your work, including your updated analysis in a larger article (while citing their paper) is a smooth way to point out how you had to change the method.

The second possibility is that many journals (at least in my area) allow for Comments on articles they have published. These are for just this purpose - to point out something 'wrong' about a paper that has been published. If the editors decide to proceed with it, the original authors are usually given an opportunity to craft a Reply piece to agree, disagree, alter, whatnot. Then they are published back-to-back in the journal.