Does the reasoning of a scientific article reflect the process the research was carried out? Most commonly not, many would say from empirical experience, but the issue has also been studied more formally:
Schickore, J. (2008) Doing science, writing science. Philosophy of Science 75:323-343.
This article investigates the mismatch between the actual process through which science is made and the way scientists afterwards communicate their results. Namely, publications do not reflect the processes through which results were derived, but rather take the results as a start point when formulating hypothesis to which the results then provide an answer. This comes close to the old discussion/debate on negative results. Scientists do not tend to publish those, yet those are derived through exactly similar research processes as the positive ones (i.e. asking questions, doing experiments etc). If the aim of scientific communication were to tell how scientists do science, then there should be no problem with negative results. However, the reality might be more close to this PhD comics.