The Gemara goes through a series of takkonos of Yehoshua relating to land use in Eretz Yisrael. Among them are 10 dinim of Yerushalayim. Yerushalayim wasn't distributed to the shevatim and therefore the dinim that would apply to other cities such as Ir Hanidachas, Eglah Arufah etc. don't apply to it.
My question is - when the land was distributed to shevatim and families in the time of Yehoshua, Yerushalayim was not yet picked to be the permanent place of the Bais Hamikdash. The mikdash went to Shilo and Nov and Givon for many centuries before Yerushalayim was chosen by Hash-m and people didn't know that it would become the place of the Bais hamikdash yet. How could Yehoshua have singled it out for this purpose at that time? It should have belonged to shevet Yehuda and possibly part to shevet Binyamin.
Sam Kosofsky
My reading of the Gemara did not indicate that the ten things said about Yerushalayim related to the Takanos of Yehoshua; it seemed like a separate list. Did you have a Ra'ayah that they were also enacted by Yehoshua?
D. Zupnik
Regarding the question of how could the Gemara say that Yerushalayim not divided among the Shevatim at the time of Yehoshua, when Yerushalayim was not yet chosen at that time - RASHI in Shoftim (1:16) explains that indeed, Yerushalayim was not specified at that time. However, the land was divided up on condition that when Hash-m would reveal which city will be home to the Beis ha'Mikdash, the tribe located in that area would give up that city and return it the public. In return, the tribe would receive the city of Yericho, which was inhabited until that time by proselytes (such as the descendants of Yisro; see Rashi there).
Regards, M. Kornfeld