Contradiction with Ezra 2:70
This verse states that all Israel lived in their cities, suggesting that not only the tribes mentioned in 1 Chronicles 9:3 resided in Jerusalem.
Ezra 2:70: So the priests, and the Levites, and [some] of the people, and the singers, and the porters, and the Nethinims, dwelt in their cities, and all Israel in their cities.
Contradiction with Nehemiah 11:1
This verse indicates that the leaders of the people lived in Jerusalem, while others cast lots to bring additional people to live there, expanding the groups beyond those in 1 Chronicles 9:3.
Nehemiah 11:1: And the rulers of the people dwelt at Jerusalem: the rest of the people also cast lots, to bring one of ten to dwell in Jerusalem the holy city, and nine parts [to dwell] in [other] cities.
Contradiction with 1 Kings 12:19
This verse indicates a division between Israel and Judah, suggesting that all Israel was not united or living in one place as might be implied by 1 Chronicles 9:3.
1 Kings 12:19: So Israel rebelled against the house of David unto this day. [rebelled: or, fell away]
Contradiction with 2 Kings 17:18
This verse talks about the Lord removing Israel from His sight, which contradicts the notion of widespread habitation of Israelites in Jerusalem in 1 Chronicles 9:3.
2 Kings 17:18: Therefore the LORD was very angry with Israel, and removed them out of his sight: there was none left but the tribe of Judah only.
Paradox #1
1 Chronicles 9:3 mentions people from the tribes of Judah, Benjamin, Ephraim, and Manasseh living in Jerusalem. A possible issue could be with other parts of the Bible that state Jerusalem belonged to the tribe of Judah. This could seem inconsistent since it suggests that members from other tribes were also settled there. However, it's generally understood that people from other tribes lived there for various reasons, so it's not necessarily a contradiction.