Again, from his POV, he doesn't think he was pickpocketed once. He found the replacement, and the kid was poisoned with something else. What reason is there for him to think he was pickpocketed the first time? Other than paranoia.
His first thought was that he'd been pickpocketed and accused Walt of poisoning Brock on the basis of that. A reasonable assumption considering how carefully he looked after the ricin cigarette and how ruthless and manipulative he knew Walt could be.
My opinion is that Jesse never really dropped this first line of thinking. He might have pushed it to the back of mind, accepting Walt's explanations reluctantly whilst giving him there benefit of the doubt; but by definition the benefit of the doubt won't ever clear that original doubt. Even when the cigarette 'turned up' Jesse never ceased to strongly suspect that Walt was involved in the poisoning of the child; his decline in mental stability is extrinsically linked with the gradual realisation that Walter White is the real monster, but nevertheless Jesse is compelled to allow the man to use and manipulate him (evidence of this is seen in the last episode when Jesse vocalises this state; he tells Walt that he knows he's manipulated him at every step, implying that he's for a long time known but was nevertheless incapable of doing anything about it).
The Lilley of the Valley revelation does little to quash Jesse's prior suspensions of Walt since he has already witnessed first hand many times Walt's ingenuity in creating elaborate situations through which to weave his particular brand of lies and manipulation. It's certainly wouldn't be beyond Walter White to orchestrate such an excuse and Jesse knows this. The cigarette turning up eventually is meaningless deep down as it's but a child's trick to put back something you've stolen in order to make it appear it was simply lost.
The important factor is that Jesse suspected Walt all along. He knew that Walt killed Mike because he's become accustomed to spotting Walt's lies. The killing of Mike is crucial to the eventual full realisation in the last episode because Walt told Jesse point blank that he did not kill Mike in just the same way he refused responsibility for the poisoning of Brock; Walt's lies about Mike represented the first time since Walt's original denial that Jesse had managed to bring his overarching suspicions from his subconscious to the forefront, and herein lies the cause of his latest catatonic breakdown.
Despite all this, Jesse still cannot bring himself to escape from Walt's mindhold over his actions. Again, the scene in the desert in the last episode indicates Jesse's residence to a life under Walt's will - Jesse begs Walt to be straight with him for once but Walt refuses, choosing instead to silently lock Jesse in his arms.
The pickpocketing of the weed is the final piece in an otherwise long and convoluted jigsaw. It's the straw that broke the camel's back causing Jesse to finally lose his shit once and for all and swear bitter revenge (not for the first time mind) on the man he blames for all the darkness in his life. It's only a stretch to believe he'd react this way if you choose to look at these scenes as a passive observer free from the emotion, suspicions, pain and paranoia Jesse is suffering from.