John Gill Commentary Numbers 35:13

"And the cities which ye shall give shall be for you six cities of refuge." — Numbers 35:13 (ASV)

And of these cities which you shall give
Of the forty eight cities they were to give to the Levites, (Numbers 35:7) ,

six cities shall you have for refuge ;
which, I think, makes it clear, that not all the forty eight cities were for refuge, only six of them.