Understanding the alignment and contributions of scientific research to the Sustainable Development Goals (SDGs) is essential for guiding global progress toward these critical targets. In this context, the study focuses on SDG 3 (Good Health and Well-Being), as it dominates the most researched SDG literature, thus providing a meaningful representation of the broader SDG research landscape. The comprehensive examination of the SDG 3-related research from 2018 to 2022 highlights significant discrepancies in publications mapped to SDG 3 between the two largest databases, Scopus and Dimensions. Despite previous studies showing Dimensions to have more coverage, the present analysis finds Scopus to report 124% more publications in this area. These discrepancies extend across various levels, including country, funder, institution, journal, and author, and have substantial implications for stakeholders relying on these data. Notably, contrasting cluster themes are discovered, with Dimensions revealing five integrative clusters and Scopus focusing on six specialized ones. This discrepancy can affect global research attention, funding allocation, institutional recognition, and SDG journal alignment. The findings emphasize the need for standardization and transparency in SDG mapping methodologies, especially as the 2030 target year approaches and progress on many 2030 SDG targets is lagging. It also highlights the importance of acknowledging and understanding these disparities at various levels of the research ecosystem. The study raises questions about similar discrepancies in other SDGs and necessitates a broader analysis that might include more databases and refine publication types. It serves as a cautionary reminder to the scientific community, policymakers, and other stakeholders about the importance of careful and comprehensive evaluation when mapping publications to SDGs.