I'm currently pursuing an M.Sc. in Europe. I am going to apply for a PhD program at an Ivy league university. I am afraid that some bad marks in the master's (especially one in a relevant subject) would affect my application.
Some background: I completed my B.Sc. in mathematics with very good marks (corresponding to a GPA of 4.0 or something close to it) in Europe and then moved to another country (still in Europe) to do a quite renowned master in theoretical physics (about 1 out of every 5 applicants was selected for this master).
Current situation: Because of several factors (moving to another country, changing subject from math to theoretical physics, different and stricter exam regulations*, having chosen to follow the most demanding courses) I got bad marks in my first semester. In particular I got the American equivalent to 2.5 in a subject which is relevant for my master thesis (and for the PhD project I would like to pursue). During the second semester my grades improved. Since I got most of the required credits, I have time to do the specific low-grade exam again during next semester (I can also do more exams to replace the bad ones according to the university regulations).
Problem: Even if I do the exam again and get a good mark, I will know the results after the deadline of the application for the PhD. So, I can't reflect my ability in that core subject (apart from my results in other exams and from my reference letters) in the application. Would it be a problem for my application? Would saying "I did bad in the first semester but I will try to make up for it in the third semester" be satisfying for such elite universities? I am very excited about the research topic and would love to work on it. I am just afraid that some bad marks could affect my chances to get in the PhD program.
Additional info: The PhD program would be in physics / theoretical physics. My B.Sc. was in mathematics but included physics exams (and I did more physics exams than average by choosing optional modules).
*here I mean that in the master's I had less time to prepare for exams (they were immediately after the end of the lectures, whereas during my bachelor's I had time between the end of lectures and the exam session). Moreover, in the bachelor's I had multiple retake exams and every retake had the same difficulty whereas here we have at most one retake and if it occurs it is more difficult than the first exam (this is an objective observation claimed by professors, I quote "you can't get a good mark at the retake" and "guys I suggest you to do the exam immediately because the retake will be way more difficult").