Stuart did the job he had always been expected to do. With the army in Northern territory, cut off from their own supply lines, they had to gather provisions by taking them from the Union army. Had he shown up at Lee's headquarters with 125 wagons loaded with supplies and munitions on June 30th instead of a few days later then his reception would have been a whole lot different. As someone else pointed out earlier, Lee had sufficient cavalry to scout the Union army. He just misused it.
All in all, my guess would also be because Jackson was no longer on the scene. One of the leaders was forever gone, and it just hadn't really sunk in to Lee's mind yet!
Had it only been the loss of Jackson the confederacy could have muddled on. But a campaign into enemy territory is a daunting enough challenge without adding an army reorganization (two corps into three), two new corps commanders (Hill and Ewell), half a dozen new division commanders, and a number of new brigade commanders, and so on, and so on. None of Ewells division commanders had worked for him before, and for the most part it was the same with Hill. With as many senior commanders as that new to their commands then confusion is to be expected. It was unfortunate timing.
You are such a slow learner. And a bit on the CS side, since you do a take-off from my post, and all the time lack the nerve to actually use my name. Go and post to those who appreciate your twisted, bought and paid for nonsense...