Nombres 1:47

But the Levites after their father's tribe were not numbered among them.

BUT THE LEVITES AFTER THE TRIBE OF THEIR FATHERS WERE NOT NUMBERED AMONG THEM. Moses had understood at the beginning of his own accord that he should not count the Levites [with the other tribes], because he had been told, And with you there shall be a man of every tribe etc.,, Verse 4. meaning that each of the tribes that were to be counted should have their prince present, and since G-d had not appointed a prince for the tribe of Levi, hence he [Moses] did not count them. Therefore he was in doubt about the Levites and did not know what to do with them. And when he had finished all those who were counted of the people, and the Levites remained alone [uncounted], the Holy One, blessed be He, explained to him that he was not to count them among the children of Israel but that he should take their sum separately, for he was to appoint them over the Tabernacle of the Testimony.
He stated ‘p’kod’ [‘number’ — in the singular] the children of Levi, 3:15. meaning that he [Moses] was to count them by himself without [the assistance of] the princes, and it was he [Moses] who called upon Aaron to be with him,, Verse 39: All that were numbered of the Levites, whom Moses and Aaron numbered etc. Thus it is clear that Aaron also participated in the counting of the Levites. Since his name was not mentioned when Moses was commanded to take that census, Ramban suggests that he joined at Moses’ invitation, see further in text of Ramban that Moses’ action was alluded to in the words of G-d. See Note 93. since he [Aaron] was the prince of that tribe, and just as the princes of Israel were [present] at [the counting of] their tribes, so was the prince of the Levites to be present when they were counted. Perhaps that is the reason for the dots [in the Torah] on the word ‘v’Aharon’ [and Aaron, in the phrase: All that were numbered of the Levites, whom Moses ‘and Aaron’ numbered], Verse 39: All that were numbered of the Levites, whom Moses and Aaron numbered etc. Thus it is clear that Aaron also participated in the counting of the Levites. Since his name was not mentioned when Moses was commanded to take that census, Ramban suggests that he joined at Moses’ invitation, see further in text of Ramban that Moses’ action was alluded to in the words of G-d. See Note 93. since his [assistance in the counting] was not by the express commandment of G-d. Afterwards, [however], when the …

והלוים למטה אבותם לא התפקדו בתוכם, as will be spelled out in detail later in verse 49 where the command not to count them with the other tribes is reported. The reason why they were counted separately was that they had never been meant to be part of the military, so that they never would have formed part of such a census. Their duties were defined in terms of their ministering to the needs of the Tabernacle.

לא התפקדו, were not counted by the officials appointed to conduct the census, nor did they count themselves. (compare Ibn Ezra on this) They had not prepared themselves as had the other people for coming to the assembly point and providing documents proving their identity and genealogy. What is mentioned in this verse all referred to the time prior to G’d announcing in verse 49 that the tribe of Levi should not be included in this census. The Levites had been awaiting instructions concerning how they were going to be counted. The reason they had reason to wonder was that the tribe of Levi had not been mentioned in the list of tribes during this entire chapter when the Torah referred to “each man per each tribe” in verse 4.

והלוים למטה אבותם לא התפקדו בתוכם, and the Levites according to their tribal affiliations had not been included in this census. The reason was that the basis of counting them was not the same; they were counted from thirty days and up instead from twenty years and up. They were also only counted from thirty years and up when they were ready to perform their duties. (Numbers 4,3). (Compare Bamidbar Rabbah 1,12)