John Gill Commentary Numbers 1:49

"Only the tribe of Levi thou shalt not number, neither shalt thou take the sum of them among the children of Israel;" — Numbers 1:49 (ASV)

Only you shall not number the tribe of Levi
That is, along with the other tribes, for it might be numbered by itself, as it afterwards was, (Numbers 3:43).

neither take the sum of them among the children of Israel ;
which confirms what is before observed: now this being the declared will of God clears Moses from all partiality to his own tribe, he doing nothing but what God had commanded him.