Why did one of my squad members disappear?

Solution 1:

This seems to be some kind of glitch. There are only a handful of permanent deaths that occur in the first Mass Effect game, and none of these deaths occur during the Rogue VI mission.

You'll probably want to either load an earlier save game or edit your save game using the gibbed editor to restore Kaiden back to the land of the living.

Solution 2:

The same happened to me. If you have a party member die, and do not clear the area before getting too far from the body. Or do not wait after the combat for them to revive, they can disappear. If you go back to the ship and select your party again they come back. It's not a permanent death situation.