As compared to the other tribes, the population of Shevet Levi was very small. It cannot be said that Hashem's presence killed them due to errors in carrying the Kelim of the Mishkan, because this census took place before Hashem delegated that task to the Leviim. The Ramban suggests that the small number of Leviim is due to the fact that the Leviim did not work hard in Egypt and Hashem only allowed those who worked hard to procreate rapidly. However, the Ramban is unsatisfied with this answer and subsequently offers another one. He suggests that Yaakov's curse to Shimon and Levi caused their low populations when they entered Eretz Yisrael. The difference was that Shimon's population was diminished by a plague while Levi's population was always low since, as the Ramban explains, the Leviim devoted their whole lives to Hashem.
The Ohr Hachaim believes that Ramban's last explanation is incorrect. First, there is no proof in the Torah that Levi's tribe was small for this reason. Second, in Divrei Hayamim it is recorded that there were 38,000 Leviim between the ages of twenty and sixty. This is greater than a four hundred percent increase over the 8,500 Leviim in this age group as recorded in our Parsha. No other tribe experienced such a great increase, so why didn't Yaakov's curse apply here as well? The Ohr Hachaim and Kli Yakar suggest that the low population was a result of the Leviim's decision for the spouses to separate, since the boys would be killed anyhow (see Sotah 12a and Shemot 2:1). This idea is supported by the statistics in Divrei Hayamim, the sudden jump of people can be the result of the Leviim deciding to return to their spouses.
The Kli Yakar gives additional reasons for the relatively small number of Leviim. First, the Leviim deliberately limited their numbers, so Bnai Yisrael would not have to strain themselves to support them (the Leviim were supported by the congregation). The Kli Yakar quotes others as saying that Hashem foresaw which Leviim would be righteous and therefore fit to serve Him. Hashem then caused those Leviim to multiply quickly; however, the impure ones were removed. This answer is supported by a quote of Chazal that says, "The Ark reduced them [the Leviim]."
Another answer offered by the Abarbanel was that the increase of Bnai Yisrael on a whole was done purposely by Hashem. The other tribes multiplied rapidly so Bnai Yisrael would have the numbers to conquer and maintain Eretz Yisrael. The tribe of Levi was supported by Maaser (one tenth of all produce), and was not allocated land, therefore, Hashem did not cause them to increase like the others.