This sentence compares the number of men identified as underpaid to the number of women identified as underpaid.
>> The study, which disproportionately led to pay raises for thousands of men
"Disproportionate" is used to signify something that is "out of proportion", in a lay sense, not in the mathematical sense of the ratio between two numbers. It is not a mathematical term that signifies a comparison between percentages, as your comment seems to suggest.
>> they received a higher percentage of the money.
This says nothing about the proportion of men or women who were found to be underpaid. It refers to the percentage of men who received more money. The justification for that is that there are more men in the company.