Well, I wouldn't call it a serious flaw. Just check all containers and you won't miss out on much. I know there's a valuable gun on the floor in Vault 15 which is hard to find (valuable at that point in the game, mind you), but for the rest, there just isn't much to be found just laying around, not stuffed away in some sort of container.
Maybe some other member knows the secret button to push to highlight all items, but I don't think there is one, to be honest.