Rashi (on 3:1) quoting the Talmud (Sanhedrin 19b) explains that the children of Aharon were also considered as the children of Moshe since Moshe taught them Torah, and this is why the Torah records the phrase "on the day that G-d spoke to Moshe at Mount Sinai" since after Moshe spoke to G-d, then he taught Aharon's children. This explanation is difficult for two reasons. One, just because Moshe taught Aharon's children, this does not end Moshe's connection with his own children, as Moshe's sons still should have been mentioned. Two, did not Moshe teach his own children as well? My son, Binyamin, suggested that Rashi’s idea is that Torah is just focusing on Aharon's sons, and Moshe is mentioned because he is also to be considered as their progenitor since he taught them Torah.
The Rashbam (on 3:1, also see Ramban on 3:1) offers a second explanation that the Torah is following the order of the general population, the priests, and then the Levites. Thus, in chapters one and two there is a discussion of the general population, 3:1-4 then discusses the genealogy of Aharon, the priestly family, and then Moshe's family is recorded in 3:27. Furthermore, he suggests that the phrase, "on the day that G-d spoke to Moshe at Mount Sinai" in mentioned in 3:1 because 3:2 records that Aharon had four sons, which was true at the time of the Decalogue, but not afterwards. This approach is difficult since 3:27 does not refer to Moshe's sons, and hence cannot be seen as the reference to toledot Moshe in 3:1. Furthermore, if 3:27 is really the reference to the phrase "toledot Moshe" in 3:1, then the phrase “elleh toledot Moshe” should have been recorded by 3:27 and not in 3:1.
A third approach (Rabbenu Saadiah Gaon and Ha-ketav ve-Hakabbalah both on 3:1) is that the phrase "these are the toledot of Aharon and Moshe" does not refer to the ensuing text but to the count of the people in chapters one and two which was done by Aharon and Moshe. Furthermore, the Ha-ketav ve-Hakabbalah suggests that the phrase "on the day that G-d spoke to Moshe at Mount Sinai" is to inform us that the count of the people was based on their numbers before the mishkan was built. This approach is difficult since when the phrase "these are the toledot" appears in the book of Bereshit in reference to people (Bereshit 6:9, 10:1, 11:10,27, 25:12,19, 36:1,9, 37:2) it always is in connection to the ensuing text, which mentions at least one descendant of the person, and not to the previous narrative. In addition, how does the phrase "these are the toledot of Aharon and Moshe" relate to the counting of the people? Were the people considered the descendants of Aharon and Moshe?
In our discussion on Bereshit, "Introduction: The structure of the book of Bereshit, " I suggested that the word toledot should be interpreted as legacy, and not descendants (https://lobashamayim.blogspot.co.il/2009/10/structure-of-book-of-bereshit.html). A person's legacy can be one's children, descendants, but it can also be one's actions in the world.
This idea suggests a fourth approach to understanding Bemidbar 3:1. In Moshe's case, while he had children, his legacy was that he spoke to G-d, and transmitted the Torah to the people. This legacy is so important that it eclipsed his children, and hence in 3:1, Moshe's children are not mentioned but instead the Torah records, "on the day that G-d spoke to Moshe at Mount Sinai" since on that day, Moshe was established as the true messenger of G-d to transmit the Torah.
With this idea, the structure of 3:1,2 is in the form of ABBA with A referring to Aharon and B referring to Moshe. 3:1 beings by referring to the toledot of Aharon (A), then mentions Moshe (B) and then records the phrase "on the day that G-d spoke to Moshe at Mount Sinai (B), which is the toledot or legacy of Moshe. 3:2 then lists the children of Aharon (A), the toledot of Aharon.
With this idea, the structure of 3:1,2 is in the form of ABBA with A referring to Aharon and B referring to Moshe. 3:1 beings by referring to the toledot of Aharon (A), then mentions Moshe (B) and then records the phrase "on the day that G-d spoke to Moshe at Mount Sinai (B), which is the toledot or legacy of Moshe. 3:2 then lists the children of Aharon (A), the toledot of Aharon.