With the caveat that this is discipline specific, you could discuss your questions in several places in your article.
First, you can begin to nod at this briefly in the methods section of your article. Every methodology has some drawback or limitation and my advisers always told me to acknowledge this in the beginning. For instance, while doing semi-structured interviews, I admitted that my sampling was convenience and snowball based and restricted to 30 participants. However, I followed this up by citing 2 papers which talk about appropriateness of sample size in grounded theory approaches and theoretical saturation and why this is not hamstringing my paper completely.
Second, one of the ways of validating qualitative studies from a methodological perspective is to look at issues of credibility, transferability etc. One of their solutions is to do member checks (especially for interview based studies) In one of my current projects, I did do member checks and talk about this approach as mitigating some of my methodological drawbacks in the Discussion section of my article.
Third, you can definitely talk about this in the limitations section of your paper. There is no panacea to solving a human-centered research problem (and indeed various nuanced facets of every research project, however thoroughly investigated they might be are almost always incomplete) In the limitations section of my papers, I put down both theoretical as well as methodological limitations of my work and discuss potential ways to approach them in future work or follow up studies.