A couple of decades ago I graduated from a Russian university with an MS in physics, and my MS thesis contained a critical flaw. In short, the thesis was about static perturbations in a certain physical system, but the system itself is unstable in the very same model, with the instability length being comparable to the characteristic size of the static perturbations in question. The whole investigation didn't make any scientific sense, because the assumed physical system can't be physically realized in the first place.
I discovered the flaw a few months before submitting my thesis. It happened rather 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.
After I discovered the flaw, I faced the dilemma as to what to do about it.
My final choice was to tell no one, even my supervisor, and simply go on to get my MS degree, deliberately failing to mention my stability analysis and its outcome in my thesis and thereby concealing the flaw. I did so because getting my MS degree asap and moving abroad for PhD studies was my highest priority. If I had raised the issue about the flaw, I would have had to start my MS project over, if allowed at all, and spend two more years to get my MS degree.
I should have performed the stability analysis at the very beginning of my MS project, but I didn't, and it's partially a fault of my supervisor, who directed my work in a very rigid way, giving me very specific tasks and deadlines. He never told me to check whether the system is stable. The official research plan, which he and I signed, did not contain any mention of a stability analysis. It was my own initiative to try to prove that the system is stable, because I felt that this was needed to make my investigation complete. I didn't even talk to my supervisor about my idea to perform the stability analysis. After I discovered the flaw, I was sure that if I talked to my supervisor about it, he would say the whole MS project had to be canceled. A product of the Soviet era, he was ruthlessly strict in terms of norms and ethics and had little compassion towards students.
After I submitted my thesis, my supervisor insisted that I write and publish an article based on the thesis. I didn't 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 later cited about 20 times. Writing that article was the most unpleasant experience in my scientific career.
To clarify, neither my thesis nor the paper claimed that the system is stable. That the system is stable was an implicit inherent assumption of the model, and it was quite a popular model at that time. The model was invented and used for other purposes well before I even started my MS project. That is, my advisor gave me a known model that no one knew to be faulty at the time, and asked me to use it for a new purpose. As explained above, I accidentally discovered and deliberately concealed that the assumption that the system is stable is wrong and can be shown to be wrong in the framework of the very same model, so the model is inherently self-contradictory regardless of the purpose of its use.
As I expected, no one found 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. In that article, I explicitly wrote that the model and all articles based on it are invalid science. I cited some articles, including my article based on the MS thesis, as examples of invalid science. No one published a comment in response. In private conversations, my colleagues confirmed that my conclusion about the flaw is correct. And the faulty model practically stopped being used after that.
Many years have passed since then, and I have built a solid career and have articles published in Physical Review Letters, even as the first author, but I still feel uneasy about the fact that I started my academic career with a misleading MS thesis and deliberately concealed the flaw in order to graduate smoothly.
I understand that what I did is a research misconduct, but the question I'm still struggling to find the answer to is whether my research misconduct was ethically justifiable under the circumstances. My colleagues say it was, but I'm unsure whether they are frank about it, so I really want to hear what other people have to say. I want truly impartial answers from people who do not know me. This is why I'm posting my question here.
Here are some additional details:
If I had not concealed the flaw, I would almost certainly have not become a scientist at all, because I could not afford two more undergraduate years in Russia. My parents didn't want to help me financially any further, so I had to get my MS degree asap and move abroad. At that time (late 1990s), living in Russia was very hard because of an economic crisis. Besides, even if I had found a way to finance the additional undergraduate years in Russia, the delay of my graduation would have harmed my chances to win the prestigious Western PhD stipend that I won.
Formally speaking, my MS thesis and the article based on it might be seen as not containing any flaw, because I was given a specific physical model and investigated static perturbations within the framework of that model as requested; the fact that the model is faulty is a separate, although related, thing. The message of my thesis was essentially that if we take that model and make those calculations, we get those results. It was a valid message per se. I was just an undergraduate student who had to do what the supervisor said. He gave me the model and requested certain calculations. I did them absolutely accurately and wrote up the results.
My MS project wasn't a significant research project anyway. It was rather a training project to learn how to do calculations and write up results. Even if the model were not faulty, the article would not have had any considerable impact. No one used the results of that project. People merely cited my paper.
The only harm due to me concealing the flaw was that a number of scientists continued using the same faulty model for other purposes, unsuspecting that the model is faulty. If I had told them that the model is faulty, they would have spent their research efforts for something more useful. But that would have put my own career in danger, because exposing the flaw too early might have resulted in a retraction of my MS degree and a subsequent termination of my PhD studies. I didn't want to take that risk.
Was my research misconduct ethically justifiable under the circumstances? Or should I have reported the flaw right after I discovered it, even at the huge expense explained above? Or what should I have done after I discovered the flaw?