I commented elsewhere that this is a major difficulty with trying to save her. Invisible Hermione would have to scream in the middle of combat to fake out the patronus, which is obviously an incredibly dangerous thing to do.

... Maybe. It still seems odd, though.

Indeed! But they would also want his non-expulsion to be plausible without revealing how important he is, nor do they want Fred and George to be expelled. I think McGonnigal is going to have to lose face here.

Harry had forgotten that he was not to use his timeturner in front of other people- a fact which got him a very stern rebuke from Mcgonagall.

When asked to find Hermione, why would Harry's Patronus have found a simulacrum instead of the real one?

The Patronus that came back to Harry could be Future-Harry's Patronus, if time travel is involved.

Note: I don't personally place a high probability on theories involving time travel in this instance, but they do present a possible explanation for that objection.

Because the real Hermione was under an invisibility cloak ten feet away. (Not saying this is how it happened, but it does explain that part of the riddle)

But in Chapter 17, McGongall rejects the theory that remembralls detect Obliviation.

“More importantly, why did the Remembrall go off like that?” Harry said. “Does it mean I’ve been Obliviated?”

“That puzzles me as well,” Professor McGonagall said slowly. “If it were that simple, I would think that the courts would use Remembralls, and they do not. I shall look into it, Mr. Potter.” She sighed. “You can go now.”

But, strange that Harry doesn't think to keep experimenting with the Remembrall.

Interesting that Harry uses his med pack he bought in anticipation of almost exactly the scenario which played out when he used it, except that Hermione absolves him instead of cursing him.

“One of my classmates gets bitten by a horrible monster, and as I scrabble frantically in my mokeskin pouch for something that could help her, she looks at me sadly and with her last breath says, ‘Why weren’t you prepared?’ And then she dies, and I know as her eyes close that she won’t ever forgive me—”

The detailed foreshadowing often seems like part of the story, not just as aspect of the story. What is said comes true much more than it should, and in much more detail than it should. "Bitten" is a very specific way to die.

... So, since this scene is obviously engineered by somebody (Harry arriving bare minutes too late, the wards not alerting Dumbledore, etc), I'm just going to go through the list of people who have shown the ability to plan such things.

a) Quirrel.

Unlikely.

The Defense Professor had felt the boy's horror, through the link that existed between the two of them, the resonance in their magic; and he had realized that the boy had sought the troll and found it. The Defense Professor had tried to send an impulse to retreat, to don the Cloak of Invisibility and flee; but he'd never been able to influence the boy through the resonance, and hadn't succeeded that time either.

He'd felt the boy give himself over fully to the killing intention. That was when the Defense Professor had begun burning through the substance of Hogwarts, trying to reach the battle in time.

This seems odd. Burning through Hogwarts is going to be a pretty big deal for him - he's basically demonstrated either an instinctive Harry-dar (and a way of knowing what Harry is doing, as well), or else he knew where Hermione was all along. Both of which are rather suspicious. I have no doubt he'll escape repercussions (Obliviating Trelawney comes to mind), but it still seems sloppy to incur them if he can avoid it.

This implies that this is simply not his plot: as he is already under suspicion and under watch, he loses nothing from a random walk that happens to put him near Hermione in case something goes wrong. And somehow, I am loathe to expect Quirrell to make a mistake while predicting the actions of another, even when that other is Harry Potter - especially when he knows that Harry has someone to defend and a killing instinct.

b) Dumbledore.

More likely, but still unlikely.

The obvious version of this plan includes Hermione dying - and for all that Dumbledore has morally greyed, I still can't see him killing a twelve-year-old girl in cold blood. (To him, I imagine, leaving her to die is a completely different matter.)

The second most obvious version of this plan - faking Hermione's death - has fewer problems, but is simply narratively unlikely. The biggest problem is Hermione's death-scream; it's a big dramatic moment, it's incredibly personal to Hermione in a way I'm not sure Dumbledore could emulate, Harry feels it cling to Hogwarts for a moment...

It's more likely than Quirrell (and certainly fits his style better - very complex and seemingly error-prone), but I'm still skeptical of ascribing any plan that pushes Harry away from the Light to Dumbledore.

c)

... We're basically out of appearing characters. That said, there's this rather interesting line...

"Lead it away, keep it off me," said a voice.

Harry, feeling disassociated from himself? No; a few seconds later we have

"Fire and acid!" Harry shouted. "Use fire or acid!"

Disassociated-Harry shows up later, I think, but that first call doesn't seem to be Harry's.

So we're looking for someone who has the manipulation ability of Quirrell and Dumbledore (but, preferably, not Quirrell or Dumbledore), already present at the scene (which means s/he knows exactly where Hermione would flee to and that Harry would follow), who doesn't want to save Hermione's life from Harry's perspective.

... At this point, I'm making an intuitive leap. We've already been suspicious that a Peggy Sue will show up; we think we know that the timeline must be consistent; we know that Harry has just resolved (and been PROPHECY-ed) to rip apart reality to bring by Hermione...

I'm wondering if future Harry - as in, really future Harry, not time-turned plus-six-hours Harry but after-the-fic plus-thirty-years Harry - hasn't shown up to pull a Chrono Trigger style rescue. We can ascribe essentially infinite competence to this Harry - by dint of living through this once (or more) times he can create the timeline he remembers, and is fully capable of a perfect illusion (for example, letting Hermione "die" and then catching her soul after it escapes, which by definition would satisfy any test Dumbledore et al could run.)

... there's probably a few flaws in my logic (I noticed after typing this that I jumped straight to "future Harry" and came up with a rationalization for it), but I didn't see anyone else proposing this, so I threw it up anyway.

We also have reason to believe Dumbledore has a motive to convince Harry that death is inevitable.

ETA: and no evidence supporting the hypothesis that what was killed is Hermione, instead of a simulacrum; we only have absurd priors that it was her, and the evidence suggests that one of our very likely priors is wrong.