Yeah, I noticed this on my first read through, and it does seem like a slip-up. However, the whole novel seems to play pretty loose with continuity, especially when it comes to flipping back and forth between worlds. There seems to be a strong theme throughout the book of questioning reality, or at least of not being able to trust things like geography, timelines, causality, and tangible objects. The style of the writing itself (with so many foreshadows, flashbacks, and jumps in time) even seems to mirror this theme. For instance, I defy anyone to construct a timeline of Jack's experiences at the Alhambra before he leaves. And, Wolf's shoes also seem to disappear and reappear during and after his first change. As for a rational explanation of Jack's shoes in the Black Hotel, certain articles of clothing are known to appear out of nowhere when someone flips into the American Territories (like Wolf's John Lennon Glasses). Maybe Jack got a new pair on one of his many flips while fighting the guardians. Unlikely, but possible.