Contradiction with Exodus 40:20
Exodus 40:20 describes Moses putting the Testimony into the ark and setting the mercy seat on top of the ark, aligning with Exodus 25:21 rather than contradicting it.
Exodus 40:20: And he took and put the testimony into the ark, and set the staves on the ark, and put the mercy seat above upon the ark:
Contradiction with Numbers 10:33
Numbers 10:33 refers to the ark going before the people to seek out a resting place, which does not directly contradict the instructions of placing items in the ark as stated in Exodus 25:21.
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 Hebrews 9:4
Hebrews 9:4 summarizes the contents of the ark, which includes a pot of manna and Aaron's rod, adding details not mentioned in Exodus 25:21 but not directly contradicting it.
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;