In a statement released today (as transcribed by As) the FFM said the following:
When the questionnaires sent by FIFA for the best player and best coach awards arrived, we contacted the captain Goran Pandev to confirm his votes for both categories. Pandev elected José Mourinho as the best coach. However, due to a technical error when the forms were processed, the box next to Vicente Del Bosque was marked. It is clear that Pandev's vote was intended for Mourinho.
Because the votes were selected electronically rather than by hand (as can be seen from the marks on the ballot that FIFA released to clear up any suggestion they might have been involved) it was always one of several explanations for what might have happened.