Discussing avoidable flaws in my work in a master's thesis
"if it matters, the data was obtained from a published paper" -- I would say that it matters a great deal. Talk about the issue, but spin it as a strength of your research (it uncovered a bias in the existing literature -- which is one of the things that subsequent research is supposed to do) instead of a weakness that you need to be apologetic about. If anyone should feel apologetic, it should be the authors of that paper and the referees who didn't notice the problem. You should feel proud about that aspect of your work. I don't know your advisor, but I wouldn't be surprised if he is impressed by this rather than critical of it.