Contradiction with John 1:46
Nehemiah 11:35 mentions Lod and Ono as places involved in rebuilding, suggesting some positive significance, whereas John 1:46 expresses skepticism about anything good coming from a certain place.
John 1:46: And Nathanael said unto him, Can there any good thing come out of Nazareth? Philip saith unto him, Come and see.
Contradiction with Jeremiah 10:22
Nehemiah 11:35 discusses settlement and building up of places, while Jeremiah 10:22 talks about desolation and the scattering of inhabitants.
Jeremiah 10:22: Behold, the noise of the bruit is come, and a great commotion out of the north country, to make the cities of Judah desolate, [and] a den of dragons.
Contradiction with Isaiah 25:2
Nehemiah 11:35 refers to people inhabiting cities, whereas Isaiah 25:2 speaks about cities being made into heaps and being ruinous.
Isaiah 25:2: For thou hast made of a city an heap; [of] a defenced city a ruin: a palace of strangers to be no city; it shall never be built.
Contradiction with Jeremiah 4:7
While Nehemiah 11:35 depicts settlement, Jeremiah 4:7 warns of cities being laid to waste and without any inhabitants.
Jeremiah 4:7: The lion is come up from his thicket, and the destroyer of the Gentiles is on his way; he is gone forth from his place to make thy land desolate; [and] thy cities shall be laid waste, without an inhabitant.