Contradiction with Genesis 11:9
Nehemiah 7:26 lists people from Bethel and Ai, locations existing post-flood, while Genesis 11:9 describes the scattering of people from Babel, which seems contradictory to re-settling specific locations so soon.
Genesis 11:9: Therefore is the name of it called Babel; because the LORD did there confound the language of all the earth: and from thence did the LORD scatter them abroad upon the face of all the earth. [Babel: that is, Confusion]
Contradiction with 1 Samuel 13:19
Nehemiah 7:26 implies settled and equipped people, while 1 Samuel 13:19 mentions there was no blacksmith in Israel, contradicting the presence of developed towns.
1 Samuel 13:19: Now there was no smith found throughout all the land of Israel: for the Philistines said, Lest the Hebrews make [them] swords or spears:
Contradiction with Deuteronomy 28:62
Nehemiah 7:26 lists a large number of returning exiles, whereas Deuteronomy 28:62 warns that few will be left if they disobey God, seeming contradictory regarding the remnant.
Deuteronomy 28:62: And ye shall be left few in number, whereas ye were as the stars of heaven for multitude; because thou wouldest not obey the voice of the LORD thy God.
Contradiction with Joshua 8:28
Nehemiah 7:26 references Bethel and Ai inhabitants, but Joshua 8:28 states Ai was a heap forever, contradicting their existence as thriving towns.
Joshua 8:28: And Joshua burnt Ai, and made it an heap for ever, [even] a desolation unto this day.
Contradiction with Judges 21:25
Nehemiah 7:26 lists orderly returnees, while Judges 21:25 describes a time of chaos and lawlessness, which seems incompatible with organized civic lists.
Judges 21:25: In those days [there was] no king in Israel: every man did [that which was] right in his own eyes.