Mahnke has stated that there's a clue to what happened to Bruce in the cowl of the costume Superman is holding when he gets the body in FC; I for one believe that the difference is in the lack of white lenses on the costume drawn by Mahnke as compared to that which Batman was killed in.
Add that to the fact that Supes is handing over a cowl with intact eyelenses, no visible damage, and black rather than blue...and you may begin to smell a rat. What does Kal know, that we don't?