The biggest problem is still companion death while entering another cell while levitating, but I also noticed that they can also disappear forever.
I recently had an issue where I was levitating with one of my companions in tow, and used scripted teleportation to get to Balmora. Now she was set to teleport along with the player using an MWSE script that allows her to follow anywhere. I heard the mysticism hit, so her script executed, but she was nowhere to be seen. Calling her with the telepathy ring revealed her to be in the same cell in wall examining mode, but calling her to initiate her warp script did nothing. Sending her home did nothing. Using a manual positioncell in the console could not even bring her to me. She was gone for good.
Now, I usually know better than to levitate while teleporting with a companion, but it just sometimes happens when you forget to let it wear off before leaving an area. It doesn't always cause trouble, but is there anything that can be done to minimize the risk?