When landing on a target point, the vehicle first burns to align the target landing spot on the selected location. Later it burns again to reduce the velocity but this causes the problem because the vehicle now will no longer land on the desired spot. This issue applies to any target spot, including the KSC pad, the VAB and any other selected spot. So it seems like it doesn't take the deceleration burn into consideration during the first burning for deorbiting.

duplicate of other bugs referenced off of #1052