From a similar level of experience, I would say that I see two common problems. The first is that there is not clear problem statement. To guide the reviewer, the purpose of the research should be clearly stated in the introductory section. Second, the literature review is often too general. The goal of the literature review should be to demonstrate the need for the current research, rather than to summarize all of the work in the field (which might be an appropriate approach in a thesis, but not in an article).

Other common problems I see sometimes are (a) mismatch in methods. Researchers may state that they use a particular analytic approach but the explanation provided in the methods section does not reflect that approach (b) or researchers claiming to have used a particular qualitative research approach (e.g., content, reflexive thematic, discourse analyses, etc.) without showing how they did it; which makes their data analysis process so abstract. Also, for co-authored works, processes are stated without indicating who did what. Although this information is often provided in the author contributions section, some information in the methods section can help reviewers to determine how certain decisions may have influenced the results.