I found published results of my mentor to be wrong. How to tell her? For the last few days, I have been trying to reproduce things in a published paper (in quite a reputed journal) from my field. My postdoc mentor is the last author of the paper and the main work was 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 the 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 my mentor this. 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 permission to write a comment about the paper? If I do either of these (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 a famous fundamental theorem. I got this confirmed from a few people in the field.)
As a matter of fact, I believe there is no such thing as guilt or ruin
for other people's work when it comes to the academic aspect of the knowledge.
Actually, if you do not share this with your mentor in order to be fixed, you 
may ruin many other further research...

I suggest you do this respectfully and carefully. You can go to your mentor and talk about this problem. You can show her your code and your understanding from the paper, then confirm whether or not you are right. Let her decide what she can do about this. There is also a slight chance you have made a technical mistake while investigating their work, so keep this in mind when you discuss the issue.