Obtaining evidence for the composition of the early atmosphere is challenging. Scientists cannot travel back in time to collect samples of gas.
Scientists use evidence from rocks and fossils which then has to be interpreted. Existing explanations about how and when levels of gases changed in the ancient atmosphere are challenged by:
New explanations are not usually accepted until more evidence is found.
Mendeleev left gaps where he predicted that elements, not discovered at the time, would fit. These elements were discovered later and closely matched his predictions. This increased confidence in Mendeleev's table and it gradually became accepted by the scientific community.
Mendeleev also had to swap a few elements so that they were still grouped with elements with similar chemical properties. The later discovery of protons led to scientists knowing the number of protons in the atoms of each element. This explained why Mendeleev had had to swap some elements around, improving upon his ideas. The modern periodic table lists elements in order of increasing atomic number.