Theory:Doctor Who television discontinuity and plot holes/The Ark


 * It's rather remarkable that the TARDIS manages to land in the same spot twice (albeit a few years apart) when the Doctor can't control its journey.
 * The Doctor forgot to enter new spacial coordinates, or there was a breakdown in the mechanism, and only the time circuits were activated for this journey. This being the case, the TARDIS followed its default/emergency procedure (See DW: Terminus) of remaining locked-on to the Ark as a 'fixed point', even though it would have moved billions of miles through space in the intervening centuries it took to reach Refusis.
 * Alternatively, given the recent revelations in The Doctor's Wife, the TARDIS may have realised that the Doctor was partially responsible for causing the Monoids to overthrow the guardians, and taken him to the future because that is where he "needed to go" to put things right.