Why was the tribe of Levi not counted together with the other tribes?
Rashi #1: Because it is befitting for the king's legion to be counted independently.
Rashi #2: Because Hashem foresaw that all those who were counted from twenty years and upwards were destined to die in the desert, so He precluded the Levi'im from that counting, 1 because, since they did not sin by the Eigel, they belonged to Him. 2
Rashbam: Because they were not conscripted to go to the army like the other tribes. 3
Seforno and Da'as Zekenim (in Pasuk 47): Because they were never counted like all the other tribes from the age of twenty, but either from one month from birth or from thirty years regarding the Avodah.
Why does the Torah insert the word "Ach"?
Moshav Zekenim: "Ach" is an exclusion. It therefore hints at the fact that many Levi'im died due to the fact that they did not treat the Aron with due respect, and that, as a result, they were the smallest tribe. 1
Seforno: Even though the Levi'im were included in the command "Se'u es Rosh Kol Adas B'nei Yisrael", they are not to be counted like the other tribes in three regards: In that 1. they are not to be counted from the age of twenty or included in the total number of people; 2 2. they are appointed over the Mishkan 3 and 3. they encamp around the Mishkan and not together with the other tribes. 4
Refer to Bereishis 29:34:154:1 & 2.
Thus explaining the dual Lashon in the Pasuk - "es Mateh Levi Lo Sifkod, ve'es Rosham Lo Sisa".
In Pasuk 50.
In Pasuk 53.