The detainee for whom the Supreme Court ruling was named, one of the six Algerians who had been living in Bosnia, Lakhdar Boumediene, was not to be among the three released, evidently because he had been stripped of his Bosnian citizenship at the time of his detention because of questions about how he obtained it.

The article doesn't mention the other Bosnian the Pentagon won't release. As to background,

After hearing a week of secret evidence in the case of the six Bosnians, a federal district judge in Washington, Richard J. Leon, ruled last month that the evidence presented by the government had not been sufficient to prove that five of the men were enemy combatants.

Judge Leon urged the administration to free the men, and not to appeal the ruling, saying that seven years was long enough for them to get a court decision. The ruling drew international attention, in part because it was the first full court test of the government’s detention evidence and because Judge Leon, considered a conservative, was an appointee of President Bush.

Were the men dangerous?

The case against the six men offered the latest example of the administration’s pattern of changing strategy in its legal defense of the detention camp. On the eve of the hearing before Judge Leon, the Justice Department said it was abandoning its claims about the embassy bombing plot. Instead, it claimed in court that the men had been planning to go to Afghanistan to fight Americans.

The defense lawyer for one of the men to be released says:

“It’s tragic that it took seven years and the ruination of their lives to accomplish this."