Not quite.
No, the FBI reports that a detainee had accused American jailers of flushing the Koran down a toilet. None of this is new information.
In other documents, FBI agents stated that Guantanamo detainees also accused U.S. personnel of kicking the Koran and throwing it to the floor, and described beatings by guards. But one document cited a detainee who accused a guard of dropping a Koran, prompting an "uprising" by prisoners, when it was the prisoner himself who dropped it.
Not much here that wasn't in the earlier Newsweek article
Pending direct witness reports, we're still in the "He turned me into a newt" zone.
Keep digging. They'll find more dirt on our military if they try hard enough.