I think the Zohar Hakadosh discusses the fact that even his bones did not go in. Also, many Mephorshim (including the ??? ????? ??’, the Chida’s Rebbi) explain that the reason for Moshe Rabbeinu being buries outside of Eretz Yisroel is to bring the Yidden back from the Galus. Also, isn’t there a Medrash about a king who tried finding the Kever, and it seemed to those on top that it was on bottom and vice versa?
An easy way out is that his physical bones did not enter but his Neshama did go through Me’aras Hamachpeila which is described as the doorway to the Olam Haneshamos.