I was trying to use Doctor to trash my Hovel in a game with Shelters, but there doesn't seem to be a way to name any of the Shelters. Presumably, this occurs at other times you need to "name a card", but the card you want to name isn't visible anywhere on-screen.
This happens with all the choice cards, you can only currently choose cards that are available, so issues Shelters/Split piles/ Mixed Piles (e.g. Knights/Castles/Ruins)
This bug is still active. Doctor still can't select Shelters even though Doctor doesn't specify that it has to be a card from the Supply.
FYI, this isn't the same as an official response, but I've created a mod that fixes this. See here:
http://forum.shuffleit.nl/index.php?topic=1380.0