Not "US prisons", but "Guantanamo", was the subject.
The pertinent passage from your link:
In the US, almost a year after the Supreme Court decided that detainees in Guantanamo should have access to judicial review, not one single case from among the 500 or so detained has reached the courts because of stonewalling by the Administration.
Under this agenda some people are above the law and others are clearly outside it.
Guantanamo has become the gulag our times, entrenching the notion that people can be detained without any recourse to the law.
If Guantanamo evokes images of Soviet repression, "ghost detainees" – or the incommunicado detention of unregistered detainees - bring back the practice of "disappearances" so popular with Latin American dictators in the past.
According to US official sources there could be over 100 ghost detainees held by the US.
In 2004 thousands of people were held by the US in Iraq, hundreds in Afghanistan and undisclosed numbers in undisclosed locations.
AI is calling on the US Administration to "close Guantanamo and disclose the rest". What we mean by this is: either release the prisoners or charge and prosecute them with due process.
In WWII, we had declarations of war against sovereign nations. That way, we could all tell who the war was against, who were The Enemy, and when the war was over.
Our declared "War on Terror" is a lot like the "War on Drugs" and the "War on Poverty": it uses the rhetoric, but we have no actual foe. Terror is an action; Drugs are a commodity; Poverty is a condition. When wars are not against organized and recognizable groups of people, but against concepts and objects, it's painfully easy to redefine the way we treat those caught in the web of violence because the old rules, conveniently, don't fit.
Amnesty International's point is that there are secret prisoners, and prisoners being held in a kind of Hell (Purgatory, only forever), because WeSaySo. Amnesty International got started in a response to secret prisoners being held for unclear reasons or for clearly political reasons. Their recent statements about US detention policies are well within the tradition of their organization.
If anyone would like to try these prisoners for actual crimes, convict them, and imprison them for those crimes in accordance with the law, Amnesty International would not have a dog in this fight.