Seeing as it is only in Pasuk 49 that Moshe is commanded not to count the Levi'im, why does the Pasuk mention it here?
Ramban: Moshe did not count the Levi'im together with Yisrael, since, when the 12 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.
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 Bnei Yisrael... " (Seforno, on Pasuk 49).