Contradiction with Numbers 10:33
While Exodus 40:21 mentions the ark being placed in the tabernacle, Numbers 10:33 describes the ark as going before the people to seek a resting place, indicating it was not stationary in the tabernacle.
Numbers 10:33: And they departed from the mount of the LORD three days' journey: and the ark of the covenant of the LORD went before them in the three days' journey, to search out a resting place for them.
Contradiction with 1 Samuel 4:4
In Exodus 40:21, the ark is placed inside the tabernacle as a resting place, but in 1 Samuel 4:4, the ark is moved out to go into battle, contradicting the idea of it remaining inside the tabernacle.
1 Samuel 4:4: So the people sent to Shiloh, that they might bring from thence the ark of the covenant of the LORD of hosts, which dwelleth [between] the cherubims: and the two sons of Eli, Hophni and Phinehas, [were] there with the ark of the covenant of God.
Contradiction with 1 Kings 8:9
Exodus 40:21 ends with the setting up of the tabernacle and the placement of the ark with its contents, whereas 1 Kings 8:9 states that only the tablets of stone were inside the ark, omitting other items that some traditions claim were placed with the ark.
1 Kings 8:9: [There was] nothing in the ark save the two tables of stone, which Moses put there at Horeb, when the LORD made [a covenant] with the children of Israel, when they came out of the land of Egypt. [when the: or, where the]