I've found what looks like a bug in Atahualpa's 404 handling. On my test installation (with a fresh copy of WordPress 3.5.2 and Atahualpa 3.7.12), when WordPress permalinks are set to the "Post name" option (in Settings / Permalinks), and when there are more than two "levels" of slashes in the URL for a missing page, Atahualpa does not display its error message ("Sorry, but you are looking for something that isn't here") and instead, it displays the contents of another page. For instance,
displays the appropriate message, but
does not. When I switch back to the Twenty Twelve theme, I get an appropriate 404 error message with both URLs. (I will leave this example up for about a week; it's a new subdomain so it may be a few more hours before DNS propagation completes.)
I am able to work around this issue by creating a custom 404 page, as Flynn describes here. But in my opinion, it would be good for Atahualpa if this issue could be fixed.
Thanks for a great theme!