From here until verse 18 is also in Nechemyah (11:1-25). There are many differences in names, lineages, numbers and other matters!
Malbim: Between "Kol Eleh Bnei Atzal" (8:38), until the end of this Parshah, "Eleh Bnei Atzal" (9:44) there were 400 camels laden with Drashos (Pesachim 62b). This is not surprising. There are many contradictions, and Ba'alei Pshat amassed 400 camels full of folly (to resolve and expound them). Nechemyah did not repeat what Ezra wrote in Divrei ha'Yamim - he added omissions and explained what Ezra did not explain, just like when Divrei ha'Yamim differs from previous Seforim, it is because Ezra wanted to add or explain something. Nechemyah (11:3) began with the same words "uvi'Yerushalayim Yashvu..." to show that he copies from here (but also adds).
Here it lists people in Yerushalayim from Efrayim and Menasheh. Why are they omitted in Nechemyah?
Malbim (Nechemyah 11:4): It was already written here, and Nechemyah had nothing to add about them. He did add about Bnei Yehudah and Binyamin. E.g. here it says "Usai ben Amihud ben Amri ben Imri ben Bani Min Bnei Peretz" (4); Nechemyah added esteemed fathers in the lineage until Peretz that Ezra omitted; he did not add fathers that were not esteemed.
