MLS manipulates Best XI to include Donovan
Donovan was on the ballot as a forward. According to MLS Commissioner Don Garber, the league felt Donovan belonged on the Best XI, so after the votes were counted, the league placed him on the final list as a midfielder. It's unclear who was bumped off (the player who received the fifth-most votes among midfielders).
They are opening up a huge can of worms here. How can we ever trust any of the awards announcements again? In 2007, Cuauhtemoc Blanco was nominated for MVP yet didn't make the Best XI in a similar situation (he was listed as a forward, along with Angel and Emilio). They didn't feel the need to change things then.
MLS need to reform the voting process, allowing for a flexible formation depending on how the votes come in. That way, this situation won't happen again. Besides, nobody uses a 3-5-2 any more. But it's clearly wrong to change things after all the votes are in and you don't like the results.