Spoilers: Nope, although I suppose it probably takes place sometime between "Home" and "Shadow"
There is some part of Sam that knows that Dean is fallible: the intellectual part of Sam. Which, admittedly, is a pretty big part of him and did get three years' worth of being all of Sam. But there is also the little-brother part to contend with, which idolizes Dean and believes he can do no wrong, and that part is battling mightily to succeed.
At present, that part is rationalizing—and, points out Sam's intellect, that part sure spends an awful lot of time rationalizing—that there was no way Dean could have known that this was anything other than your garden-variety haunting. Dean, after all, can deal with poltergeists with his eyes shut and one hand tied behind his back. In fact, it had been so straight-forward that Sam had slept through Dean's research, had barely woken in time for the hunt, and had trusted him implicitly that all was—and would be—well.
They'd finished a job in Colorado, were aimlessly headed north (because Sam wasn't up for west towards California and Dean flat-out couldn't handle east to Kansas, and they'd flipped a coin to decide north-south) when Dean had stopped for gas in the middle of nowhere, Wyoming, leaving Sam asleep in the front seat of the Impala, and had overheard talk of strange happenings. He'd walked across the only street in town to the library, and had quickly investigated the haunting. The essentials? Sam had been told, upon waking in the front yard of a farmhouse, that it was up for sale; the realtor was freaked out (weird noises, furniture being rearranged overnight); nearly burned down in 1942; three people had died inside the house—one in childbirth in 1912, one of pneumonia in 1957, and one of suicide in 1999; clearly the suicide's spirit need to be laid to rest; the body was cremated but it obviously wasn't enough; let's go.
The adult in Sam, on the other hand, is more than willing to blame Dean for the fiasco. Dean knows that things are rarely what they seem, that whatever can go wrong will go wrong, that readiness is all. For all his impetuousness, Dean knows that success is proportional to the amount of time spent in preparation. That knowledge is power, that being able to think on your feet doesn't make a bean of difference if you haven't got the necessary equipment handy.
The intellectual part of Sam takes a time-out to muse wryly that Sam's internal battle is a lot like the one he'd fought at eight, when he and his friends had declared that, when they grew up, they'd play in the NHL, for the Detroit Red Wings, because the Winchesters were loosely based in Pontiac that year. Sam knew perfectly well that he would never be a professional hockey player, but he rejected the adult voice in his head and clung to the childish fantasy because it was normal.
Sam reflects on this, and he wonders if the very definition of normalcy is fallibility, because his father demands perfection and we want what we can't have. John can't have normalcy because Mary is dead and so he's after faultlessness—faultlessness in everything, from the condition of his car to the behaviour of his boys; and Sam, forced into that life of rigid unfailingness, reaches desperately for the ordinary.
Sam thinks he's being brilliant and he wants acutely to share his epiphany with Dean, although he knows Dean would think he was overanalysing the situation. Dean never analyses anything that has already happened—you can't change the past, dude—or at least that's what he wants Sam to believe.
So Sam decides to hold his tongue, at least until he's figured out how Dean fits into this framework. He stares out at the big sky of Montana and realizes that he already knows the answer. Dean has equated loyalty with perfection—being true to your family, unswerving, unwavering—and while his family drinks it up like the elixir of life (John's military background agreeing with the logic perfectly; Sammy thriving under his big brother's protectiveness), they don't offer it in return. And Dean wants nothing more than to receive in kind that faithfulness, so much so that his greatest fear is abandonment, and not without reason. It's happened three times, on a large scale—Mom to death, Sam to Stanford, Dad to God knows where these past few months—but hundreds of times during his childhood, too. There's the frequent absences of his father, often without warning or explanation, leaving the brothers alone for days at a time. There's the more figurative desertions of Sam to other worlds via books; neither boy had ever managed to make many friends because of their transient lifestyle, and so Sam spent most of his free time reading. Dean, who had never managed to get reading, no matter how many books Sam recommended to him, took it personally that Sam would rather read than play with him.
And suddenly Sam realizes that he and Dad are more alike than not, in all the ways that matter, which is why they both get along with Dean like a house on fire, but also why they rub at each other the wrong way, without even trying. Because opposites attract and likes repel. Why do they call it a cliché? Because it's true.
"What in the who now?" says Dean, glancing over, and only then does Sam realize he's been speaking aloud. He flushes.
"Um, well, I was think—shut up," he warns, cutting off the joke before Dean can voice it. "About us, as a family—" Dean shoots a hard look at his brother, and Sam can actually see his brother's guard go up, his shields rise, and he rolls his eyes. Dean says Sam is the sensitive one, but Sam's pretty sure that Dean feels things more strongly than Sam, it's just that he's afraid of his emotions and cuts off any sort of emotional situation at the pass so they don't ever get the change to rise to the surface, because Dean doesn't actually have a good handle on them at all.
"Just… listen, okay? Please?" And Sam's a master manipulator and is fully aware that Dean will do whatever Sam wants if he begs.
Dean gives a terse nod, and Sam tries to gather his thoughts. And all at once he's overwhelmingly tired—tired of thinking, tired of driving, tired of life—and he simply says, "Dean, I just, I just want you to know that… that I'm sorry. About Stanford. I mean, about my leaving, to go to college."
Sam sees Dean's grip tightening on the steering wheel, sees his knuckles whiten and his biceps flex. They drive a few minutes in silence, and for the first time Sam notices that there isn't a cassette tape playing. Dean's apology for the hunt gone bad?
And finally Dean's shoulders relax and he glances quickly at Sam, relief evident on his features, and he says those words that never come out of Dean Winchester's mouth, like I'm sorry and Help me and I love you: "Thank you, Sam."