I think there were several factors. The first is that communication between armies isn’t good at the best of times – look at what happened when Jaime and Tywin (or Jaime’s cavalry and Jaime’s infantry) got separated, for example. Unless both parties have a rookery that both know to write to (and even then, ravens can go awry), you’re down to riders trying to get across hundreds of miles of very dangerous territory. This only gets more complicated when Robb takes the goat path into the Westerlands and is essentially behind enemy lines, or when Roose is on the march from the Twins to Harrenhal and isn’t near a rookery.

The second is that communications can be controlled. Roose is in a very good opportunity to dictate the narrative of how the Green Fork went down, and when he’s both at the Twins and Harrenhal, he can control what goes out by raven. You would need a subordinate to have recognized that Roose intentionally threw the battle rather than making a forgiveable mistake, be willing to be wholly insubordinate by informing on his commanding officer to the king in violation of chain of command, and then get a rider all the way to Robb Stark without being noticed, and be believed when that rider gets there. 

The third has to do with expectations and perceptions. Roose Bolton stayed within the general framework of his orders at the Green Fork – he made a bunch of bad tactical choices, from failing to carry through with his night march to leaving the high ground to firing on his own men, but he didn’t violate Robb’s orders, and most importantly, Roose’s actions achieved the intended strategic effect by engaging with Tywin and allowing Robb to relieve Riverrun before Tywin could move to block him. So Robb doesn’t have any reason to perceive what happened at the Green Fork than the necessary sacrifice he thought it was.

Likewise, when Roose takes Harrenhal, he could plausibly say that A. it was the major enemy asset in the theater of war so it was good sense to take it, B. an allied commander had asked him to do it, and C. he wasn’t given orders to the contrary. Robb doesn’t have any reason to see this action as treasonous, and indeed the victory helps to obscure the pattern of Roose’s actions. It also helps that Robb is a bit distracted by Edmure’s actions at the time. 

It’s not until Duskendale that Robb has something that really rings false, and Robb immediately picks up on it, recognizing that Duskendale is a target of no strategic value:

When they brought him word of the battle at Duskendale, where Lord Randyll Tarly had shattered Robett Glover and Ser Helman Tallhart, he might have been expected to rage. Instead he’d stared in dumb disbelief and said, “Duskendale, on the narrow sea? Why would they go to Duskendale?” He’d shook his head, bewildered. “A third of my foot, lost for Duskendale?”

But here’s where Roose’s control of communications kicks in. Sitting at Harrenhal, Roose is the one sending Robb information about what happened. So Roose constructs an alternative narrative in which he had nothing to do with Duskendale:

“Your Grace is too kind. I suffered grievous losses on the Green Fork, and Glover and Tallhart worse at Duskendale.”

“Duskendale.” Robb made the word a curse. “Robett Glover will answer for that when I see him, I promise you.”

“A folly,” Lord Bolton agreed, “but Glover was heedless after he learned that Deepwood Motte had fallen. Grief and fear will do that to a man.”

Robb has no way of knowing this isn’t true, because Roose made sure that the men who could have contradicted him were either killed or captured. The only people present when Roose gave the orders to take Duskendale – through a raven, so it’s not like any of the men at Harrenhal could have talked to Glover’s army and heard about new orders, and even then those men were almost all Freys and Bolton men by that point – were Arya and Qyburn. 

The only, only way Robb could have heard differently is if Robett Glover had turned the ship around at Duskendale and headed for the Twins instead of White Harbor and gotten there ahead of the Red Wedding. Even then, odds are that Robett would have been seen as a rash incompetent looking to excuse his folly by making a scandalous accusation at his forgiving commanding officer. 

But even if Robb had believed Robett, the 5,000 Stark loyalists in Roose’s army were dead or captured, and Roose and Walder had Robb outnumbered two to one. The damage was already done.