Or HaChaim on Numbers 2:33/אור החיים על במדבר ב׳:ל״ג

1 והלוים לא התפקדו…כאשר צוה ה׳ את משה, and the Levites were not counted among them as G'd had commanded Moses. Even though the count of the Israelites represented a spiritual elevation for them as described in Bamidbar Rabbah,2 nonetheless the Levites were not counted together with the other tribes of Israel seeing G'd had so commanded. At that time the angels were described as descending together with G'd's שכינה on Mount Sinai and they inspired the Israelites to ask for flags similar to what they observed among the angels.