These were rumours and no one really knew what happened.
For example, Eddard, who actually was at King's Landing when (Or just a few hours later) this happened. Even he thinks of it as rumours.
Unlike his brother, Ser Gregor did not live at court. He was a
solitary man who seldom left his own lands, but for wars and tourneys.
He had been with Lord Tywin when King's Landing fell, a new-made
knight of seventeen years, even then distinguished by his size and his
implacable ferocity. Some said it had been Gregor who'd dashed the
skull of the infant prince Aegon Targaryen against a wall, and
whispered that afterward he had raped the mother, the Dornish princess
Elia, before putting her to the sword. These things were not said in
AGOT - Eddard VII
If even people who were there to observe the immediate aftermath of the act don't know it for sure, we can safely assume that no one did. But of course Gregor's own men must have known, his comrades too possibly who may have had the opportunity to witness the Princess' corpse. And we know that Mountain's men are prone to bragging about his rapes as they did with him raping the daughter of an innkeeper after the Hand's Tourney in front of Arya and other soldiers. So word naturally spread, which we can expect was especially fast as the rumour was about the former Queen-to-be, A Princess of Dorne and her tragic death.
Robert later ordered an inquiry but it was just a show, he was not going to break off his Lannister alliance, so it's not a surprise that it did not establish anything.
"Wars and weddings have kept us well occupied, Prince Oberyn. I fear
no one has yet had the time to look into murders sixteen years
stale, dreadful as they were. We shall, of course, just as soon as
we may. Any help that Dorne might be able to provide to restore the
king's peace would only hasten the beginning of my lord father's
"Dwarf," said the Red Viper, in a tone grown markedly less cordial,
"spare me your Lannister lies. Is it sheep you take us for, or fools?
My brother is not a bloodthirsty man, but neither has he been asleep
for sixteen years. Jon Arryn came to Sunspear the year after Robert
took the throne, and you can be sure that he was questioned closely.
Him, and a hundred more. I did not come for some mummer's show of an
inquiry. I came for justice for Elia and her children, and I will have
it. Starting with this lummox Gregor Clegane . . . but not, I think,
ending there. Before he dies, the Enormity That Rides will tell me
whence came his orders, please assure your lord father of that." He
ASOS - Tyrion V
Here, as you can notice, Tyrion does not mention the rape when he speaks of a new inquiry, neither does Oberyn. Elia and her children being murdered was undisputed, the rape however remained just a rumour. Oberyn still could have insisted on investigation of those charges as well but for some reason it did not happen.
Between themselves, when discussing the justice, Tyrion and his father talked only as if the murder charges were the only ones that Oberyn knew of for sure and even at that, he did not have any evidence as to who was the real culprit.
“Very well, as you ask so pleasantly. The Red Viper is not going to be
pleasant, I fear... nor will he content himself with Ser Gregor’s head
“All the more reason not to give it to him.”
“Not to... ?” Tyrion was shocked. “I thought we were agreed that the
woods were full of beasts.”
“Lesser beasts.” Lord Tywin’s fingers laced together under his chin.
“Ser Gregor has served us well. No other knight in the realm inspires
such terror in our enemies.”
“Oberyn knows that Gregor was the one who...”
“He knows nothing. He has heard tales. Stable gossip and kitchen
calumnies. He has no crumb of proof. Ser Gregor is certainly not about
to confess to him. I mean to keep him well away for so long as the
Dornishmen are in King’s Landing.”
“And when Oberyn demands the justice he’s come for?”
“I will tell him that Ser Amory Lorch killed Elia and her children,”
Lord Tywin said calmly. “So will you, if he asks.”
“Ser Amory Lorch is dead,” Tyrion said flatly.
“Precisely. Vargo Hoat had Ser Amory torn apart by a bear after the
fall of Harrenhal. That ought to be sufficiently grisly to appease
even Oberyn Martell.”
ASOS - Tyrion VI
But the rape did happen, Tywin Lannister, Commander of the men who did it, is confident that it happened. He however claims that he never intended to harm Elia and she should have been unharmed.
His father shrugged. “I grant you, it was done too brutally. Elia
need not have been harmed at all, that was sheer folly. By herself she
“Then why did the Mountain kill her?”
“Because I did not tell him to spare her. I doubt I mentioned her at
all. I had more pressing concerns. Ned Stark’s van was rushing south
from the Trident, and I feared it might come to swords between us. And
it was in Aerys to murder Jaime, with no more cause than spite. That
was the thing I feared most. That, and what Jaime himself might do.”
He closed a fist. “Nor did I yet grasp what I had in Gregor Clegane,
only that he was huge and terrible in battle. The rape... even you
will not accuse me of giving that command, I would hope. Ser Amory
was almost as bestial with Rhaenys. I asked him afterward why it had
required half a hundred thrusts to kill a girl of... two? Three? He
said she’d kicked him and would not stop screaming. If Lorch had
halfthe wits the gods gave a turnip, he would have calmed her with a
few sweet words and used a soft silk pillow.” His mouth twisted in
distaste. “The blood was in him.”
ASOS - Tyrion VI
But later, Tyrion admitted in front of Oberyn that the rape did happen and who was the rapist, confirming his doubts.
"How sad for him," said the Red Viper. "And for you. Do all noseless
men lie so badly, I wonder?"
"I am not lying. Ser Amory dragged Princess Rhaenys out from under her
father's bed and stabbed her to death. He had some men-at-arms with
him, but I do not know their names." He leaned forward. "It was Ser
Gregor Clegane who smashed Prince Aegon's head against a wall and
raped your sister Elia with his blood and brains still on his
"What is this, now? Truth, from a Lannister?" Oberyn smiled
coldly. "Your father gave the commands, yes?"
ASOS - Tyrion IX
So by the time Oberyn met Gregor, he was certain and he needed only Gregor's confession, which he did receive.
- There were only rumours.
- Lannisters believed Martells had no proof.
- Rape did happen.
- By the time Oberyn met Gregor in combat, he was certain about the rape and that Gregor had done it, thanks to Tyrion.