Contradiction with Joshua 3:17
This verse describes the Ark of the Covenant remaining stationary in the middle of the Jordan, contradicting Numbers 4:6's instructions to cover the Ark completely for transportation.
Joshua 3:17: And the priests that bare the ark of the covenant of the LORD stood firm on dry ground in the midst of Jordan, and all the Israelites passed over on dry ground, until all the people were passed clean over Jordan.
Contradiction with 1 Samuel 6:19
This verse details the Lord striking people for looking into the Ark, which is unrelated to carrying or covering the Ark directly, but implies a contradiction in procedures surrounding the Ark in Numbers 4:6.
1 Samuel 6:19: And he smote the men of Bethshemesh, because they had looked into the ark of the LORD, even he smote of the people fifty thousand and threescore and ten men: and the people lamented, because the LORD had smitten [many] of the people with a great slaughter.
Contradiction with 2 Samuel 6:6-7
When Uzzah touched the Ark to steady it, God struck him dead, contrasting with the careful transport procedures outlined in Numbers 4:6.
2 Samuel 6:6-7: And when they came to Nachon's threshingfloor, Uzzah put forth [his hand] to the ark of God, and took hold of it; for the oxen shook [it]. [Nachon: also called Chidon] [shook it: or, stumbled]
Contradiction with 1 Kings 8:8
It mentions the staves being seen from the holy place, indicating they were not covered, contradicting the prescription to cover the Ark and its accessories in Numbers 4:6.
1 Kings 8:8: And they drew out the staves, that the ends of the staves were seen out in the holy [place] before the oracle, and they were not seen without: and there they are unto this day. [ends: Heb. heads] [holy...: or, ark]
Contradiction with Hebrews 9:4
This refers to the Ark containing specific items which isn't directly discussed in Numbers 4:6, but shows differing focuses on what the Ark's purpose and handling involve.
Hebrews 9:4: Which had the golden censer, and the ark of the covenant overlaid round about with gold, wherein [was] the golden pot that had manna, and Aaron's rod that budded, and the tables of the covenant;