Lehi and Nephi never mentioned which tribe they were from other than to say that they were of Joseph (1 Nephi 5:14). It is only through Amulek that we learn that they were through Manasseh. Not all the Nephite blood was through Manasseh. Joseph Smith taught that in the 116 lost pages, the genealogy of Ishmael was given to be through Ephraim. Also, we know that Mulek was of Judah. Therefore, among the Nephites and Lamanites, there were descendants of Ephraim, Manasseh, and Judah.
Erastus Snow
"The Prophet Joseph Smith informed us that the record of Lehi was contained on the one hundred sixteen pages that were first translated and subsequently stolen, and of which an abridgment is given us in the First Book of Nephi, which is the record of Nephi individually, he himself being of the lineage of Manasseh; but that Ishmael was of the lineage of Ephraim, and that his sons married into Lehi's family, and Lehi's sons married Ishmael's daughters, thus fulfilling the words of Jacob upon Ephraim and Manasseh in the 48th chapter of Genesis [verse 16] which says: 'And let my name be named on them, and the name of my fathers Abraham and Isaac; and let them grow into a multitude in the midst of the earth.' Thus these descendants of Manasseh and Ephraim grew together upon this American continent, with a sprinkling from the house of Judah, from Mulek descended, who left Jerusalem eleven years after Lehi, and founded the colony afterwards known as Zarahemla found by Mosiah -- thus making a combination, an intermixture of Ephraim and Manasseh with the remnants of Judah, and for aught we know, the remnants of some other tribes that might have accompanied Mulek. And such have grown up upon the American continent." (Journal of Discourses, vol. 23, pp. 184, 185)