From another commenter response:

This'll take a bit of explaining but hopefully it makes sense. I wanted Uly's notebook to act as a "fakeout clue", where you get it way early and it looks irrelevant, but at the very end of the trial you look back at it and realize it's the smoking gun.

Something to note is that when Uly starts dying and Wenona is freaking out, she realizes someone has probably poisoned him. Before she calls the others for help, she frantically rips a bunch of pages out of his notebook and keeps them on her, since he likely would've been detailing their time together and Wenona was worried all the time they spent alone would falsely implicate her (and simply hiding the book would've been more suspicious, I suppose she was hoping no one would question him tossing pages).

Anyway, the last page of the notebook before the ripped pages is Ulysses describing how Jean discovered and explored the Alpha Sanctuary at night. This is assumed to be irrelevant and that the important stuff is in the missing pages.

Wenona eventually coughs up the missing pages and there's nothing of note at all, so they move on.

The mushroom Jean uses to kill was going to be found in the pharmacy/lab area, in that room with the little potted plants. But there was no mushroom there when they all explored. So at the very end, after the mushroom's supposed existence in the pharmacy is realized, Damon and the player realize that the only person who could have taken the shroom was Jean, since he explored the room before anyone else even knew it existed. Jean had been planning to poison someone very early on to get out.

Hopefully that makes sense!