When Zeniff’s people were attacked on the south of the land of Shilom they fled to the city of Nephi, not to the city of Shilom. The city of Shilom would have been closer, but was not the seat of the government, and was probably not as large. The people fled to the seat of their people, the city of Nephi. The description of people fleeing fields into a town for protection underscores the reason for that time of organizational structure. This is precisely what is expected of the outlying farming communities. They are more vulnerable, but the city itself has the protection of a concentration of people, and probably some fortifications.
Geographic: When the original treaty was signed with king Laman, it was the land and city of Lehi-Nephi that was given to Zeniff (Mosiah 7:21). Now, however, Zeniff’s people flee to the city of Nephi. Were they two different places? There is really too little information to be conclusive. As noted, Sorenson equates the two.