Experimental use of purified diets led to identification of other essential components of the diet. Classical chemical extraction gave fractions based on solubility.
These "substances" proved to be mixtures, and as the components were separated and identified sometimes the same substance was discovered and named multiple times by eager, competing investigators. The gaps in the numbers for the B-vitamins as we know them today are because higher numbers for vitamins that had already been discovered and numbered were subsequently dropped.
This was a period of identifying the substances essential to life. It is largely over, but the essentiality of some materials has been recognized only recently (e.g., chromium, 1977, in a patient receiving total parenteral nutrition -- a "purified" diet; vanadium, 1987). Still other elements, like lead, tin and boron, are waiting in the wings (there is enough evidence to warrant further study of their essentiality).