Originally Posted by Bronco X
I've been rewatching the entire series so a lot of details have been fresh in my head... it actually makes complete sense that Jesse made the connection.
1) Jesse has already suspected that Huell had lifted the ricin cigarrette off him and Walt was involved in the poisoning. He stated his suspicions as such when he went to confront Walt about it at the end of season 4. Walt was the only other person other than Jesse who knew about the ricin. Walt convinced Jesse Gus was behind it as an attempt to manipulate Jesse into not only signing off on sending Walt to Belize, but doing it himself.
2) Later it turned out Brock had been poisoned by Lily of the Valleys not ricin and the police suspected it was an accident. Gus is dead and there is no longer reason to suspect he was involved in the poisoning, and Jesse is unnerved about the whereabouts of the ricin cigarette. Walt came over to help find it and planted a fake ricin cigarette in the Roomba. At this point Jesse still trusts Walt.
3) Drew Sharpe, Mike and the 10 prisoners are murdered, and Jesse's trust in Walt has eroded. Walt lies to Jesse about Mike and Jesse knows it.
4) Huell again lifts a joint off Jesse to make sure the Hachi's Quick Vanish guy doesn't call off the vanishing because of it. When Jesse realizes it, his original suspicions immediately resurface, coupled with his new found perspective on what Walt is capable of, he realizes not only was the ricin lifted earlier but Walt's helping him find the fake one in the Roomba was a ruse.
It's not entirely clear to me, but I think a large part of the 'aha' moment is that not only did Huell lift the pot, he might have actually replaced it with the ciggs (just like he did when he swiped the ricin containing pack) -- which if that is the case makes it much more plausible that Jessie would figure it out.