Maybe the planted shoes have pedia-egg, or some other kind of foot-grater built into the sole there. Or maybe it was a signal - 'you'll know which Locke I am by my shoes.'

Maybe they're going to try to have both Jacob and Facob be fake-Christian at diff. points, and feel one would have to have the body and one the shoes. They do sometimes get themselves in writing quandaries (though the Black V. White theme was set up pretty early) - perhaps they want to keep some of Christian's actions as Jacob's.