Theory:Doctor Who prose discontinuity and plot holes/The City of the Dead


 * The Doctor finds the bone in the TARDIS, yet at a much later stage for both the Doctor and the TARDIS, the bone is placed inside the TARDIS. It doesn't matter that this happened at an earlier date as far as Earth linear time is concerned. For the Doctor and the TARDIS, the bone was placed in the TARDIS long after the Doctor found the bone in the TARDlS.
 * The TARDIS is already known to have pockets of slow and fast time. Clara and the TARDIS implies that it can mess with the linear flow of time to some extent, so maybe the TARDIS moved the bone backwards in time to avoid the paradox.