This is going to be a long post but I believe is the only way to understand my situation.
I studied B.Sc in Information Systems Engineering in a small private university in Latin America, it's not a research oriented institution and thus does not have a high reputation, especially outside my country. My GPA is very high (here grades range from 0 to 100; I have a 84.5 GPA which is top 12~15% of the class).
After having completed my first degree I wanted to study M.Sc in Computer Science, in a different university, much larger and public-founded, that has a relatively good reputation worldwide(ranks consistently among top 300 universities in the world).
To get into the program I was asked to complete some supplementary courses and get a certain minimum grade average. On my first semester I got good grades BUT I ran into some serious trouble in one final exam.
In this final exam, I fell asleep and arrived a few minutes after the exam had started, with all the hurry and all I forgot to take my phone out of my pocket (It's forbidden to have a phone on you during test). One of the exam supervisors noticed it and I was found guilty of academic dishonesty (which meant I had no chances of continuing towards this degree). I was pissed off but instead of quitting, i pursued another degree, in the same university but in a different faculty. I pursued M.Sc in Information Systems Engineering.
To be able to get into this new program, I was asked again to complete some supplementary courses, this time I got excellent grades and didn't run into any problems. Now I'm about to start my first semester in the M.Sc, and I started to think about PhD.
So finally I can ask the question: will this incident affect my chances of getting into a good PhD program? I mean if I wanted to go abroad say to study in the US, will this incident hurt my chances beyond repair?
Edit: Possibly a new issue has arised. I started to worry about being rejected from this M.Sc., even if I completed all the sumplementary courses with grades higher than requested?
After this incident had ocurred and after the discipline hearing in which I got "disqualified" instead of the actual grade as punishment, I applied to this different M.Sc program at the same University.
I did send an email to one professor that is in the acceptance comitte of this different Masters program, asking about my chances of getting into the Masters(I didn't mention this incident, I just asked if I stood a chance).
He replied with the list of supplementary courses but now that I think about it, he probably didn't even look at the current transcript of the university, He probably just look over the transcripts of the B.Sc.
I mean I have with me a letter (which I received after the hearing) that says: You have to complete all these courses with minimum GPA of X, which I did, and every grade has to be no less than Y, which I also did.
Should I be worried?