Seeing as it is only in Pasuk 49 that Moshe is commanded not to count the Levi'im, why does the Torah mention it here?
Ramban: Because Moshe did not count the Levi'im together with Yisrael, since, when the twelve Nesi'im were nominated, the tribe of Levi was not included. 1
Seforno: It teaches us that, not only were the Levi'im not counted together with the rest of Yisrael by the counters, but that the Levi'im themselves did not prepare themselves to be counted - because, when they saw that they were not included in the list of Nesi'im, 2 they waited to see what would transpire with regard to them.
Rashbam: Here the Torah is teaching us that the Levi'im were not to be counted together with the other tribes; and the Torah goes on to tell us why - because whereas the other tribes were being counted to prepare them to go to war, the Levi'im were being counted in order to serve in the Mishkan.
Oznayim la'Torah: According to the Teshuvas ha'Rosh, 13:21, who explains that the prohibition against drinking wine preceded the death of Nadav and Avihu - even though it is only written after it, based on the principle 'Ein Mukdam u'Me'uchar ba'Torah', 3 we can say here too, that the current Parshah was actually told to MOshe before the Mitzvah to count Yisrael.
Ramban: In fact, based on that omission, he initially thought that perhaps they would not be counted at all, and was in a quandary what to do with them - until Hashem informed him (See 3:15) that it was only together with the other tribes that they were not to be counted, but that they were to be counted independently.
See above, Pasuk 5-16. And this, in spite of the fact that they were included in the initial command (in Pasuk 2) "Se'u es Rosh Kol Adas B'nei Yisrael... " (Seforno, on Pasuk 49).
See Oznayim la'Torah, who, citing the Teshuvas ha'Rosh, elaborates.
