Contradiction with Numbers 1:20
This verse states that the descendants were counted by their lineage and not absorbed into other tribes, which contrasts with Genesis 48:6 where Jacob adopts Joseph's sons into his own family line.
Numbers 1:20: And the children of Reuben, Israel's eldest son, by their generations, after their families, by the house of their fathers, according to the number of the names, by their polls, every male from twenty years old and upward, all that were able to go forth to war;
Contradiction with Deuteronomy 21:17
This verse stipulates the rights of the firstborn son to receive a double portion, which contrasts with Genesis 48:6 where Jacob gives prominence to Joseph's younger sons.
Deuteronomy 21:17: But he shall acknowledge the son of the hated [for] the firstborn, by giving him a double portion of all that he hath: for he [is] the beginning of his strength; the right of the firstborn [is] his. [that...: Heb. that is found with him]
Contradiction with Numbers 26:1-2
In this verse, the children of Israel are numbered according to their tribes, seemingly contradicting Genesis 48:6 where Joseph's sons receive a distinct inheritance separate from others.
Numbers 26:1-2: And it came to pass after the plague, that the LORD spake unto Moses and unto Eleazar the son of Aaron the priest, saying,
Contradiction with Ezekiel 47:13
This verse states that the land shall be divided according to the tribes of Israel, implying traditional tribal distinctions which Genesis 48:6 appears to alter by giving Joseph's sons status as heads of tribes.
Ezekiel 47:13: Thus saith the Lord GOD; This [shall be] the border, whereby ye shall inherit the land according to the twelve tribes of Israel: Joseph [shall have two] portions.