Why twelve stones, when some of the tribes already had their land east of the Jordan?

The chapter gives the reason itself, twice: "according to the number of the tribes of the children of Israel" (4:5, 4:8). The men were "a man out of every tribe" (4:2, 4:4), chosen ahead of time: at the river's edge Joshua had told the people, "take twelve men out of the tribes of Israel, for every tribe a man" (3:12), and 4:4 calls them "the twelve men whom he had prepared". So every tribe had a stone, including Reuben, Gad and the half-tribe of Manasseh, whose land lay "beyond the Jordan" (1:14) and whose men "crossed over armed before the children of Israel" (4:12). The book comes back to this later. When those tribes go home, they build an altar by the Jordan out of concern that "In time to come your children might speak to our children" (22:24) and say, "You have no portion in the LORD" (22:25).