Here the unknown scribe 2 of the original manuscript initially wrote “had come up”, then he erased come and corrected it to gone. The correction was not clearly done, with the result that Oliver Cowdery copied the word as come into the printer’s manuscript. Only in the 1981 LDS edition has the reading “we had gone up” been restored.
The text consistently refers to Nephi and his brothers as “going up to Jerusalem”, never as “coming up to Jerusalem”:
The use of go rather than come is appropriate since Nephi and his brothers are going towards Jerusalem—either away from their encampment in the wilderness or away from “the land of their inheritance”, which is outside the city walls.
Summary: Nephi and his brothers always “go up” rather than “come up” to Jerusalem.