In Shemot 40:35, Moshe was not able to enter the Tent of Meeting, only Aharon and his sons were anointed to enter. In Vayikra 1:1 Hashem spoke to Moshe from the Tent of Meeting. How was this possible since Moshe was not allowed to enter the Mishkan when the cloud rested above it, indicating Hashem's presence?
When Hashem called to Moshe, that was a command to enter the mishkan and speak to Hashem. Even Moshe Rabbeinu could not enter unless he was first invited into the Presence of Hashem.
As an example we see The Mishkan And The Mikdash cites R’ Yehuda Herzl Henkin shlita (a posek and educator in Israel) as asking
Why does the Book of Shmot end this way? We can understand why Bereishit ends where it does–at that point a line is drawn between the history of the Patriarchs and the history of the nation that came from them. The Books of Vayikra and Bemidbar also have logical conclusions–specifically, both end with the summary, “These are the commandments that Hashem commanded Moshe to [teach] Bnei Yisrael on Har Sinai.” But why is the statement at the end of Shmot that Moshe could not enter the Mishkan separated from the statement at the beginning of Vayikra that Hashem called Moshe to enter?
R’ Henkin explains: After all the work that Moshe did to bring about the construction and assembly of the Mishkan, we could almost take it for granted that he would be called to enter it. It was coming to him, one might say. One could even think that it was his (Moshe’s) Mishkan. That is why the Torah separates the call for Moshe to enter the Mishkan from the story that came before. We are being taught that Hashem called Moshe because He wanted to, not because He had to. Hashem has no need to call to any man, not even one as great as Moshe. (She’eilot U’teshuvot Bnei Banim IV p.131)
Similarly Hearing the call
In the first situation we see how the Clouds of Glory responded to the initiative of Moshe. While in the second they proved to be an obstacle.
This obstacle is removed in the first verse of the book of Leviticus;
And He called to Moshe( VaYikra), and Hashem spoke to him from the Tent of Meeting...(Leviticus 1:1)
We then see
Yet the relationship has gone through a large and critical change. The entry into such a relationship needs to be in answer to the invitation and can never be taken for granted. And He called to Moshe (VaYikra) and Hashem spoke to him from the Tent of Meeting (Leviticus 1:1). The invitation has been heard before as well. And Hashem G-d called (VaYikra) to man, and He said to him "Where are you?"( Genesis 3:9). Instead of responding to that invitation, Adam begins to spout excuses and rationalizations.
When Moshe heard the call he entered.
See Bemidbar 7:89:
My translation of text:
"When Moshe came to the Tent of Meeting to speak to Him, he heard the voice speaking to him from upon the curtain that was on top of the Ark of Testimony, from between the two cherub. He spoke to him."
Rashi explains that the voice came down from heaven went through the area between the 2 cherubs and exited towards the Tent of meeting (i.e., the area outside where the ark was placed, namely, the Kodesh Kadashim. So, it's clear that Moses was allowed to enter the Tent of Meeting, not the inner most area - the Kodesh Kadashim.