Here's a possible explanation from John Gill's Exposition of the Bible. (Sorry about the wall of text. I copied and pasted it as is.)
This pot held an omer, which was more than three pints and a half; some say six pints: and though Moses does not call it a golden pot, yet it is so called, not only by the Septuagint in (
Exodus 16:33 ) but also by Philo the Jew
F7; nor is it reasonable to think, with some Jewish writers
F8, that it should be made of earth, which was to continue for ages to come: this also was wanting in the second temple
F9; and this, with Aaron's rod, after mentioned, and other things, is said to be hid when the ark was, and along with it
F11: but how this pot, as well as Aaron's rod, can be said to be in the ark, when it is asserted, at the bringing of the ark into the temple, at the dedication of it by Solomon, that there was nothing in it but two tables of stone, (
1 Kings 8:9 ) (
2 Chronicles 5:10 ) and both the pot of "manna", and Aaron's rod, are said to be before the testimony, (
Exodus 16:34 ) (
Numbers 17:10 ) and not in it, is a difficulty. Some, in order to remove it, observe, that the phrase, "wherein", refers not to the ark, but to the tabernacle; but since the tables of the covenant were in the ark, and these are mentioned with it, and the phrase, "over it", in the next verse, cannot be understood of the tabernacle, but of the ark, this solution is not satisfactory. Others have observed, that they might be in the ark in Moses's time and in Jeremiah's time, when they are said to be hid, though they were not in Solomon's: and others have taken notice, that the preposition (en) sometimes signifies "at", or "with", as in (
Colossians 3:1 ) (
John 1:28 ) (
Ephesians 6:1 Ephesians 6:2 ) and so the sense is, that these were near unto it in the most holy place, and might be in the sides of it, though not within it; for there were places in the sides of the ark to put things into, (
Deuteronomy 31:26 ) (
1 Samuel 6:8 ) . And certain it is from the above account from Scripture, that they were near it; and so, by the Jewish writers, they are always mentioned along with it: when that was carried away, and hid, they were hid with it; but what a certain Jewish commentator
F12 observes on (
1 Kings 8:9 ) is so express, as if it was designed to vindicate our apostle: his remark is this:
``the intention of this is not to deny that there were not the things mentioned in the law, for they were (Hebrew letters) , "left in it", as Aaron's "rod", and "the pot of manna", only to deny, hereby, that there was not anything of the law, save the decalogue.''
And it should be observed, that it is not said of these, that they were put before the ark, but "before the testimony"; that is, before the tables of the covenant, which were within the ark....
Source:
Hebrews 9:4 Commentary - John Gill's Exposition of the Bible
