Yeah I've gotten this too. The first time it was after I beamed to my ship. My ship briefly appeared in spacedock, then my avatar was floating in space. The second time was when I beamed to a ship for an away mission. My ship was sitting there with 3 security officers for a while before my avatar and boff loaded.
I have seen the same thing, and submitted a bug report. When I beamed down to the Vega colony to fight the Borg, a little version of my ship was there instead. Moving around eventually made my avatar appear. When I beamed up to my ship, my avatar was standing out in space.
Later I went to meet Admiral Quinn, and the room was full of tiny spaceships