Density functional theory (DFT) is a commonly used methodology favored by experts and non-experts alike. It is a useful tool for the investigation of atomic, molecular and surface systems, offering an efficient and often reliable approach to calculate ground state properties such as electron density, total energy and molecular structure. However, fundamental issues are not rare. Of course, no one can really question the bold impact of DFT on modern chemical science. It is not only the way research is conducted that has been influenced by DFT, but also textbooks, datasets and our chemical intuition as well. In this review, issues pertaining to DFT are discussed, and it is pointed out that without a clear understanding of why we use calculations, an effective combination of experiment and theory will never be accomplished. Using low-level theoretical frameworks surely does not shed light on profound problems. To excel in our scientific field and make good use of our tools, we must very carefully decide which methodologies we are to employ.