Twelve Main Tribes of Israel
Gen 49:28 All these are the twelve tribes of Israel, and this is what their father spoke to them. And he blessed them; he blessed each one according to his own blessing.
The twelve main Tribes of Israel are the descendents from the twelve sons of Israel (Jacob) as follows:-
1. Reuben - Gen 49:3
2. Simone - Gen 49:5
3. Levi - Gen 49:5
4. Judah - Gen 49:8
5. Zebulun - Gen 49:13
6. Issachar - Gen 49:14
7. Dan - Gen 49:16
8. Gad - Gen 49:19
9. Asher - Gen 49:20
10. Naphtali - Gen 49:21
11. Joseph - Gen 49:22
12. Benjamin - Gen 49:27
Exo 39:14 There were twelve stones according to the names of the sons of Israel: according to their names, engraved like a signet, each one with its own name according to the twelve tribes.
Exo 32:26 then Moses stood in the entrance of the camp, and said, "Whoever is on the Lord's side—come to me!" And all the sons of Levi gathered themselves together to him.
Because the Levites chose to be on God's side, God chose them to serve only Him in the tabernacle. Since God was the inheritance of the Levites, they were not allowed to any earthly inheritance.
Num 18:20-21 Then the Lord said to Aaron: " *You shall have no inheritance in their land, nor shall you have any portion among them; I am your portion and your inheritance among the children of Israel*. Behold, I have given the children of Levi all the tithes in Israel as an inheritance in return for the work which they perform, the work of the tabernacle of meeting."
Inheritances in Canaan Land
Eze 47:13 Thus says the Lord God: "These are the borders by which you shall divide the land as an inheritance among the twelve tribes of Israel. Joseph shall have two portions"
Since the Levites could not have any earthly inheritance, the Promised Canaan land (besides those set aside for God's temple, etc.) would be given to the rest of the eleven tribes.
Jacob gave the birthright (normally reserved for the eldest son) to Joseph who inherited double portion. So the inheritance will again be given to twelve tribes - eleven main Tribes with the tribe of Joseph splitting into two subtribes of Manasseh and Ephraim.
The Armies of Israel
Num 1:1-4 Now the Lord spoke to Moses in the Wilderness of Sinai, in the tabernacle of meeting, on the first day of the second month, in the second year after they had come out of the land of Egypt, saying: "Take a census of all the congregation of the children of Israel, by their families, by their fathers' houses, according to the number of names, every male individually, from twenty years old and above —all who are able to go to war in Israel. You and Aaron shall number them by their armies."
The armies of Israel comprised of ten main tribes plus the two subtribes of Manasseh and Ephraim. The Levites were exempted from military service for they had no earthly inheritance and they served only in the tabernacle of God.
Num 1:47-49 But the Levites were not numbered among them by their fathers' tribe; for the Lord had spoken to Moses, saying: "Only the tribe of Levi you shall not number, nor take a census of them among the children of Israel"
Truth of Twelve Tribes of Israel
So whenever the tribe of Levite is included in the twelve tribes of Israel, then the tribe of Joseph is also mentioned, for these are all the descendents of the twelve sons of Jacob.
For inheritance, the tribe of Levite will be missing from the twelve tribes and the tribe of Joseph will be replaced by its subtribes of Ephraim and Manasseh.