Weird that he was sold but Hernandez will be loaned, apparently.
Do we have a buyback clause or something?
He probably wanted to leave.
Louis van Gaal might have mentioned possible future plans and they could have involved 4-3-3 (point forward) with Rooney second striker and RVP up top so Mata drops to the bench, also Januzaj in a season or two would be competing for the role behind the striker if they buy quality on the wings.
Furthermore he may have stated there is also the possibility of him playing with the point backwards (E.g. Strootman and Herrera in front of a Carrick like player) depending on the availability in the transfer market.
All in all, he expects Kagawa to have strong competition for his position in the team. I would imagine he does not fit his profile for a winger, he would have likely told him this and so Kagawa might have decided he would be better off on the bench at Dortmund where there is a much better chance of him establishing himself.
Who knows, of course I am guessing here but at the age Kagawa is and the ability he seems to have he might want a lot of game time. He had the chance to join a club that is challenging both domestically and in Europe, a team that is far superior to United in this moment and probably will be at least for another 2 or 3 seasons.
It's possible actually a lot of the United squad would not get into the Dortmund first team so if he manages to do this then he has done well.