Thank you, my dear friend, for such an excellent question!  The answer to this is interesting, but a bit complicated.  I’ll begin with Levi.  Levi was indeed the father of the tribe of Israel called by that name, but as to the inheritance in the land of Canaan when the children of Israel returned after the captivity in Egypt, Levi was to have a very special inheritance apart from a portion of the land—the LORD Himself was to be their portion.   We read in Deuteronomy 18:1-2: “The priests the Levites, and all the tribe of Levi, shall have no part nor inheritance with Israel: they shall eat the offerings of the LORD made by fire, and His inheritance. Therefore shall they have no inheritance among their brethren: the LORD is their inheritance, as He hath said unto them.” Thus, Levi was indeed a tribe of Israel, but their lot was the priesthood of God, and in this was their inheritance in terms of their role and their sustenance.

Now, Joseph was also a son of Jacob and indeed, he was the father of his tribe, but Jacob, while he was dying, blessed the sons of Joseph, Ephraim and Manasseh, and took them for his sons and gave Joseph a double blessing, each of the two sons receiving a land inheritance and to be fathers of individual tribes of Israel. In Genesis 48:1-22, you can read the entire story, which is very interesting indeed. You might recall that Jacob himself had been blessed by his father above Esau, even though he was younger, because it was the sovereign will of God; and in Genesis 48, we see the same happening with Ephraim and Manasseh, with Ephraim getting the blessing over his older brother. I’ll cite a couple key verses, “

(1) And it came to pass after these things, that one told Joseph, Behold, thy father is sick: and he took with him his two sons, Manasseh and Ephraim. (5) And now thy two sons, Ephraim and Manasseh, which were born unto thee in the land of Egypt before I came unto thee into Egypt, are mine; as Reuben and Simeon, they shall be mine. (6) And thy issue, which thou begettest after them, shall be thine, and shall be called after the name of their brethren in their inheritance. (22) Moreover I have given to thee one portion above thy brethren, which I took out of the hand of the Amorite with my sword and with my bow.”

In summary, Levi and Joseph were certainly sons of Israel (Jacob), and both are included in the “twelve tribes of Israel.” However, with Levi having an inheritance apart from land, God Himself being their inheritance (as priests of Israel), the twelve tribes were completed by Joseph getting a double portion, one each for Joseph’s two sons.  You’ll note in the Scriptures that there are always twelve tribes, the names of the tribes depending on whether you are talking about the sons of Israel themselves, or their inheritance in Canaan. Wm. MacDonald in his commentary on Genesis 48 says: “The dying patriarch sat up on the bed and adopted his two grandsons as his own. By doing this he arranged that the tribe of Joseph would receive a double portion of the land of Canaan when it would be divided among the tribes years later. Joseph thus received the birthright as far as territory was concerned. Any offspring born to Joseph after them would be Joseph’s, not Jacob’s, and would dwell in the territories allotted to Ephraim or Manasseh.”  (SF)  (589.6)