The cloud covered the Ohel Moed, and the glory of Hashem filled the Mishkan. Moshe was unable to enter the Ohel Moed, because the cloud rested on it, and the glory of Hashem filled the Mishkan. (40:34-35)
Here are some thoughts about this cloud.
Ohel Moed vs Mishkan
The "Ohel Moed" and "Mishkan" are general names for the sanctuary, but each name also refers to one specific part of the sanctuary.
In the initial command to build a sanctuary, Moshe is told to "make curtains of goat-hide, for an 'ohel' upon the 'mishkan'" (26:7). Here, the "mishkan" is a cloth tent, and the "ohel" is a goat-hide tent placed upon it.
This explains the different uses of "ohel" and "mishkan" in the above verses. The cloud *above* the sanctuary is described in relation to the ohel, and the cloud *within* the sanctuary in relation to the mishkan.
The purpose of the cloud
This cloud wasn't a normal thing. It prevented anyone from entering the Mishkan, but normally, priests would enter the Mishkan at least once a day to perform services like lighting the Menorah. So why did this special one-time cloud appear?
To explain this, let's look at an earlier, similar event involving a cloud:
Moshe went up to the mountain, and the cloud covered the mountain. The glory of Hashem dwelt on Mount Sinai, and the cloud covered it six days, and He called to Moshe on the seventh day from out of the cloud. The appearance of the glory of Hashem was like fire burning on the peak of the mountain, in view of the children of Israel. Moshe entered the cloud, and went up the mountain, and Moshe was on the mountain for forty days and forty nights. (24:15-18)
There are a number of similarities between this cloud and the cloud that covered the Mishkan:
- In both cases, an unusual cloud descends to cover the holy site. (Apparently Mount Sinai had previously not been covered by clouds, despite the involvement of clouds in the Sinai revelation).
- With the Mishkan, a "cloud" was present above the Mishkan, while the "glory of Hashem" was present within the Mishkan. Similarly here, the "glory of Hashem" dwelt on the mountain, while the "cloud" covered the mountain. Both terms are present, and arguably there is the same order, with the "cloud" physically above the "glory of Hashem".
- At Sinai, after six days of Moshe waiting outside the cloud, God calls to Moshe and he enters the cloud and receives the Torah. Similarly, in the Mishkan, God calls to Moshe. This command is found in the first verse of Vayikra, and is followed by the laws of sacrifices.
What is the point of these similarities?
One of the main purposes of the Mishkan is described in Shemot 25:21-22:
"You shall place the cover upon the ark, above it; and in the ark, you shall place the Testimony I will give you. I will meet you there, and I will speak with you from above the cover, between the two cherubs upon the ark of testimony, all that I shall command you regarding the children of Israel."
We see that the Mishkan was a place for revelation. The Sinai revelation was a one-time event, but the continued issuing of commandments (like those in Vayikra) was supposed to occur in the Mishkan.
I think this explains the similarities between the cloud at Sinai and the cloud at the Mishkan. To indicate to Moshe and the people that the revelation from the Mishkan had the same status as that at Sinai, God designed the cloud-appearance in the Mishkan to evoke that which occurred at Sinai.