Contradiction with Exodus 3:12
This verse suggests God's presence will be confirmed by serving Him on a different mountain, whereas Genesis 46:3 reassures Jacob about going to Egypt.
Exodus 3:12: And he said, Certainly I will be with thee; and this [shall be] a token unto thee, that I have sent thee: When thou hast brought forth the people out of Egypt, ye shall serve God upon this mountain.
Contradiction with Isaiah 31:1
Warns against trusting in Egypt for help, yet Genesis 46:3 encourages Jacob to go there.
Isaiah 31:1: Woe to them that go down to Egypt for help; and stay on horses, and trust in chariots, because [they are] many; and in horsemen, because they are very strong; but they look not unto the Holy One of Israel, neither seek the LORD!
Contradiction with Deuteronomy 17:16
Advises against returning to Egypt, contradicting God's instruction in Genesis 46:3 to not fear going there.
Deuteronomy 17:16: But he shall not multiply horses to himself, nor cause the people to return to Egypt, to the end that he should multiply horses: forasmuch as the LORD hath said unto you, Ye shall henceforth return no more that way.
Contradiction with Jeremiah 42:19
Explicitly tells the people of Israel not to go to Egypt, opposing the reassurance given to Jacob in Genesis 46:3.
Jeremiah 42:19: The LORD hath said concerning you, O ye remnant of Judah; Go ye not into Egypt: know certainly that I have admonished you this day. [admonished...: Heb. testified against you]