Hmm, I haven't noticed one, but I also haven't tried to mine downwards, to be fair.

[ Sigh, he feels like he's missing something terribly obvious. ]

Downwards...downwards from the puffin's nest besides the sewers... The back entrance to JojaMart isn't downwards. The wizard tower does have a basement with this weird magic circle. The mines? [ He goes down a list in his mind, trying to remember which places have some form of downstairs area. ] I wonder what else would count as down for the puffins? They are pretty tiny.