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He originally made her to be a grail that malfunctions because he is just copying the Einzberns' methods and forcing her body to gain resiliency through suffocation, poisoning, and torture methods, also trying to break her mind, so she would succumb to being the grail and be the vessel, it came to the point that nothing he could do externally fazed her and she wasn't fooled by him. In the flashback scene in HF, Bailing Hand, on day 9 right after Shirou decides to protect Sakura and goes back to the Church, it showed how the AM connection came out.
It connected what happened after Sakura pales when seeing the mark of the chosen on Shirou and why she gave Rider to Shinji, besides the fact she didn't want to fight. However, this time Zouken has met with Shirou and now has a better idea of how to use both Rin and Shirou against Sakura. It was her fear after seeing his mark of the chosen and her distrust that Rin would not kill him that spawned that tiny spark of genuine malice that caused the contract to accidentally happen, the gate to open, and for the taint to start flowing into Sakura, making her a malfunctioning Lesser Grail. Basically, Zouken's trolling got a response he desired, by getting at the chinks in her armor. The conversation had him luring her in by saying she didn't have to kill all the masters she defeated, and could keep a couple as pets if she wanted, Sakura sees his game and refuses, saying she would give Rider to Shinji anyway, since she has no idea what he'll do if she agrees to fight. And then things would go like they would in the other routes by her making the book and that being the end of it, except for then Zouken trolls her as I said above and the gears move into motion that make her a Lesser Grail. That is pretty much the difference between HF and the other routes, Zouken uses as much leverage as he can and gets lucky as the stars align.
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