I just see that as their purpose... Paul Thompson said in 9/11: Press For Truth, there really is no difference between an "Al-Qaeda" training camp, and an ISI training camp.
Read 'Ghost Wars' by Steve Coll. A thorough and excellent work on Afghanistan and the ISI. I agree with the original post concerning Pakistan. Another indicator would be the wiring of funds to Atta by the then head of the ISI just before 9/11.
Of course this link was never followed up in the commission. After the India Times started questioning this the head stepped down.
Then of course is the fact that the CIA created the ISI.
The CIA/ISI connection is far too tight for that. Not to mention that the Atta/Pakistan was never investigated. Can't see the US ever attacking Pakistan.