The U.S. has found that al Qaeda has been using Afghan prisons as a recruiting and training venue. This should come as no surprise, as American and European counter-terror officials have found the same phenomenon in local prisons. The problem showed up in Iraq as well. Last year, it was noted that several dozen of the 100,000 or so Iraqis who had been held in U.S. prisons in Iraq over the previous five years, have been murdered by Islamic terrorists while in prison. The killings were done to enable the Islamic radicals to gain control over the more moderate inmates. This makes it easier for the Islamic radicals to plan attacks on guards, or even escape. Such control also provides the militants with better living conditions, at the expense of the prisoners they have intimidated. Finally, the radicals find it easier to find new recruits.
This is not a new problem. American military police first encountered it during World War II, when hard core Nazis, among German prisoners of war, got organized and terrorized the other prisoners, including "executions" of those who put up the most resistance. Their goals were the same as the Islamic terrorists. During the Korean War (1950-53), Chinese and North Korean prisoners did the same thing, with the communist true believers terrorizing everyone in the name of "party discipline." Same deal during the Vietnam war.
The fix for the intimidation problem has always been the same; more careful screening of prisoners. This is easier with military prisoners, as it's easier to identify who is who. But with irregulars (as in Vietnam and Iraq), the hard core types will try to hide their true beliefs. These guys always have to deal with the possibility that they will end up in a part of the prison where they have few friends, and many people who don't like their kind, and are inclined to express their feelings violently.
The hard core prisoners also try to recruit less enthusiastic cell mates to a more fanatical position. But in most cases, the best the hard case prisoners can do is impose a reign of terror among their less motivated cell mates, and exploit them.