I got stuck on the last two flowers when I first played this last night, and came back to it today determined to complete my flower book, which I did after a lot of time! Yay!
It took me some thinking to first realize that both images needed to be of legitimate flowers that were new, so that it wasn't possible to unlock the thousand-petal daisy unless I also found the butterfly flower. The flower checking mechanic was explained in the tutorial but because it's such a new and unintuitive mechanic to me I still didn't expect it to work like it did, and it was frustrating when I was sure of a new flower but it wasn't finding it because I didn't have a second new one to pair it with.
I think the mechanic would have become more intuitive if after flower checking you could click straight to the flower book with a highlight on the new flowers, so you could see that you'd added two different ones and which ones those were. Navigating out to the main menu, back into an area, and then to the flower book, felt clunky every time and by the time I got there I'd forgotten what was new. Especially early on when I was unsure whether every variation of the sprites counted as a different kind of flower, as with the different petaled daisies.
It also might have helped if when the flower checking failed it gave a reason, letting you know something like "One of these flowers is a 3-petaled daisy. That's already in your flowerdex!" or something like that.
There was no hint for the butterfly flower, and I don't know whether that was because the thousand petal daisy was required to unlock the hint and I was unlucky in leaving those two for last, or whether it was meant to be a mystery, or whether it's a bug.
Then I realized it's possible to have the photos be in two different areas, which opened up all four areas as potential hiding places for the butterfly flower. I took a long time to be sure I wasn't missing anything, and then I put on my lateral thinking hat to consider what a game developer might do for a last, secret, special flower given the mechanics available. I tried a few things before I thought of the mechanic you used, but once I thought of it I was sure that's what you'd done. The first places I checked were the areas above other flowers, and areas of open sky, because that's where butterflies would be. But then I thought you probably wouldn't hide it randomly, so it had to be somewhere special, and that cave had been waiting around unused. And the cave was also conveniently behind the photo UI, so you wouldn't be able to find it just by clicking around randomly while looking at the images, and the game had already shown itself to not want to reward random clicking.
So... I got there in the end. But I do feel a little like that extra difficult flower came out of nowhere, and I wouldn't expect any but the most unreasonably stubborn player to find it.
I did like the game though, especially the sound design, as it made it more pleasant to spend time playing.