וְהַלְוִיִּם--לֹא הָתְפָּקְדוּ, בְּתוֹךְ בְּנֵי יִשְׂרָאֵל
the Levites were not numbered among the children of Israel ... Bamidbar 2:33
all those numbered are Levites ... Bamidbar 4:46
It seems clear that the Levites were not numbered among the children (as a subset) of Israel because the Levites are numbered as representative of the entire set of Israel. This is not such an enigma. It's mathematics.
There are alot of numbers in this Torah portion, which is why in English the book of Bamidbar is called Numbers as we all know. Maybe Bamidbar should be subtitled Studies In Advanced Set Theory.
That's all folks.