Both woodshed and woodpile are used. In the Southern US, the saying tended to mean that something was either wrong or highly unusual about some situation.
“something (as a concealed motive or obscure factor) contrary to appearances in a situation”
“The judge’s eyebrows rose. But he only grunted. He thought: Indian Island, eh? There’s a nigger in the woodpile.”
Agatha Christie, And Then There Were None
