Nobody can really tell what has transpared between Victor Boniface, BayernLeverkusen and AC Milan for that move not to work, AC Milan didn't come up with a full report saying it was the medical result that made them to call off the deal, because if they want to say it was the medical that he faild, what then did Werder Bremen use to ascertain his fitness for them to agree for a loan move. The national call for World cup qualification is entirely a different thing, not all players will be invited in some cases but I don't think it has to do with his medicals.
Maybe AC Milan and Werder Bremen have different medical standards. The Italian side was concerned about his past injury history, which includes previous knee injuries and two cruciate ligament tears. This might also be a cover-up of their inability to afford the financial obligations or other reasons. The good part of the story is that Victor Boniface has gotten a deal with a top club. All he needs to do now is work hard to prove AC Milan wrong.