I placed my boat in the mine, placed a crate full of ore in it, and now it wont let me take out the crate or lift the boat. I tried right clicking it in several different positions, and also lifting it.
When a canoe is placed on land, it is upside down. You cannot retrieve items stored in a canoe unless it is right-side up on the water, since otherwise they will be hidden from view and not clickable.