In the last two Raider attacks I've seen my dwellers in another room, on a lower level of the vault, slowly die while Raiders are fighting dwellers at the vault entrance room. In the last instance, six dwellers in the clinic two levels down slowly died while the three Raiders were in combat on the top level. Any ideas what's going on here?

I think it happens if there are spaces in the first and 2nd floor. I had a vault where I had only 1 room on the top floor and then started building my vault from the 3rd floor and experienced this as well

I've only had this happen once. The game seemed to think deathclaws were in a completely different room than they appeared to be. I assumed it was just a random glitch. I was still able to keep them alive with stimpaks, until the deathclaws died. Easy not to notice its happening until too late, though.