For last few days, I am trying to reproduce things in a published paper (in a quite reputed journal) from my field. My postdoc mentor is the last author of the paper and the main work has been carried out by her collaborators from a different institute and a first author is finishing his Ph.D.

When I saw the paper, I immediately got skeptical because they had missed some obvious things. So I rewrote all code from scratch and after a week’s extensive checking and cross-checking, confirmed that their results are completely wrong. I told two of my trusted colleagues and they asked me to tell this to my mentor. However, I am quite uncomfortable and confused about this.

The student who is the first author has based a big part of his later work on these results. This means that the later work by the student might also be completely wrong. My question is how to proceed from here? Can I ask my mentor to retract their paper? Or should I ask her the permission for writing a comment about the paper? If I do either of this (or something else which reveals that those results are wrong), would I be considered guilty of destroying the thesis of the first author guy?

I really appreciate any type of help in this matter. Thanks in advance.

Edit: All the answers and comments here are very helpful and I thank you all for them. However, I think I was slightly vague while asking. I very well understand that I could be certainly wrong. But the question is what do I do if I am not? In that case, what should be done? (As things stand, they have surely got at least one plot wrong because it directly goes against some famous fundamental theorem. I got this confirmed from few people in the field.)

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