I've been trying to recreate this bug in my game and It seems to me this only happens in "outside" areas like Gilded Vale or Caed Nua. When I go to the Temple of Eothas in Gilded Vale or inside the keep at Caed Nua I can't seem to recreate the bug. I'm not 100% sure on this, because it needs allot more testing, for all I know it could still affect your companions at other "inside" locations but I am gonna assume it's allot less buggy to save "inside" then saving "outside".
*EDIT* Typo.