Or HaChaim on Numbers 1:3/אור החיים על במדבר א׳:ג׳

1 תפקדו אתם, "you shall number them." The reason the Torah repeats this instruction, something which is contained in the command of "count the people" in verse two, is explained by Yalkut Shimoni on this verse as connected with the jealousy the Gentile nations would display when they became aware that G'd deemed only the Jews worthy of being counted individually. G'd would counter their complaint by inviting them to produce books tracing each family's genealogy. If they were able to do so they too would qualify for a census based on family affiliation as was being conducted amongst the Israelites. This is why G'd employed the expression שאו when He first commanded the Israelites to be counted; He told them that being counted was a form of elevation, promotion, for them as implied in the word שאו, "elevate, uplift!" Subsequently G'd explained in verse three that the males above the age of twenty were so elevated. It follows that the words תפקדו אתם are necessary to describe the actual commandment to count the people.