I believe they were made up to trap Cersei, yes.
My theory is as follows:
Margaery was not acting when she was first told what happened to Loras. Aurane Waters tells Cersei the tale and smiles when Cersei insists on telling Margaery. He smiles because they have her.
Margaery was told by Cersei and believed it - her initial reaction was genuine as were her tears.
Read the chapter again: that same night after Margaery is told by Cersei about what supposedly happened to Loras - Lady Merryweather leaves Cersei's bedchamber and goes to spend the evening with Margaery and her maid to "comfort them" instead. It is then that Lady Marryweather tells Margaery the truth to "comfort her" and bring Margaery into the Queen of Thorns' machinations.
Look back on all the information that Cersei is given regarding Margaery and her virginity, the Blue Singer, who she sees, etc. It all stems from information Lady Merryweayther gives Cersei. Cersei's "independent investigations" are all undertaken only after the seed is first planted by Taena. It is Lady Merryweather who remember's Renly's erection that wedding night, that Margaery is no virgin, etc.. Lady Merryweather also tells Cersei that Pycelle has been spending a great deal of time with Margaery as well - and Cersei walks right into it and asks Pycelle what - where he confesses: "I provide Her Grace with sleeping draghts and ... other sorts of potions."
Pycelle was set up and the door is opened - and Cersei walks right into it.
Later in open court after Margaery is arrested, Cersei asks Pycelle to go to Baelor's Sept to verify her virginity, instead of going herself to speak with the High Septon. Pycelle goes white and admits to the moon tea in open court.
That's all it takes - the council is dissolved and off Cersei marches. But as she does, Lord Merryweather and Aurane Waters immediately move to justify launching of the fleet. An accident? Come on! Read it again!
Cersei readily agrees. (And off Aurane Waters goes to get the fleet battle ready and cast off).
The next day, before Cersei goes to the High Septon, it is Lady Merryweather who asks about what happens if Margaery asks for a trial by combat. Taena is ready to suggest the answer to Cersei if our Golden Fool fails to see it - but Cersei takes the bait and off to the High Septon she goes. But before she goes she once again invites Lady Merryweather's son to court - and once again is declined.
GRRM is telling us - once more - that Taena is a traitor.
Margaery plays her part and reminds Cersei that Loras is hurt. That done, Margaery tells the "vile, scheming, evil bitch" to leave.
The High Septon does not confront Cersei with Osney Kettleblack until after Cersei has said that it must be a member of the King's Guard who must defend the Queen. When she says that - they have her. The next thing he says is that Cersei may not leave.
The same timorous Pycelle who confessed to giving Margaery moon tea is shortly thereafter busy running the kingdom and calling for Kevan Lannister within an hour of Cersei's arrest by the High Septon. The fleet which was readied for battle by the comments of Lord Merryweather and Aurane Waters is off to sea and the defence of Highgarden.
Cersei was played the entire time - and Loras' "injuries" are an integral part of it. Without Loras being injured, any trial by combat would go in Cersei's favor. They played her for a fool the entire time. Who is "they"? The Queen of Thorns and Littlefinger.
Why is Qyburn let in to see Cersei? So that she does not suspect the whole of the truth, else she might puzzle it out and recognize Loras is not injured - and see her one route of escape. So Qyburn tells Cersei what they want her to believe: that Aurane Waters has gone off to be a pirate or to Stannis (anywhere but Highgarden) and the Merryweathers - true friends of Cersei that they are - have now fled the city to avoid the wrath of Cersei's enemies ascendant.
Cersei, more the fool, thinks that Taena fleeing to Longtable is a sign of her loyalty and a stroke of good fortune. She sees what they want her to see and misses all the clues to the truth.
So, to recap: what's in it for the QoT?
1 - She must preserve Margaery from Cersei;
2- She must get rid of her without provoking the Lannisters or deposing Tommen. This is vital because the urgent need is for the Royal Fleet to save Highgarden *right now* which stands exposed to the Ironborn. All of this must be done in such a way as to avoid a war with the Lannisters.
In order to do this, she must use the High Septon - a man who cannot be bought. To do this, she must risk Margaery (without really risking her).
And so Lady Taena Merryweather and the Kettleblacks (and through them, LF) play their game.
It's all about this: Get Cersei to say to the High Septon that the Queen must rely upon the Kingsguard to defend her against a charge and with the Blue Singer's tale - Cersei is damned. Osney Kettleblack sings a tale as well? So much the better, but the Blue Singer was the intended informant. Osney Kettleblack was just a bonus.
As long as Loras is "hurt", Cersei is deposed without risking war with the Lannisters.
So what is in it for Littlefinger?
As it turns out, what's in it for Petyr Baelish is nothing less than the Rule of the Seven Kingdoms.
It was Jaime's suggestion of settling on Baelish as the perfect Hand to appease the Tyrells that got me thinking...
"If Cersei can be put aside, Ser Kevan may agree to serve as Tommen's Hand. And if not, well, the Seven Kingdoms did not lack for able men. Forley Prester would make a good choice, or Roland Crakehall. If someone other than a westerman was needed to appease the Tyrells, there was always Mathis Rowan...or even Petyr Baelish. Littlefinger was as amiable as he was clever, but too lowborn to threaten any of the great lords, with no sword of his own. The perfect Hand." - Jaime Lannister, AFFC, page 667.
This leads me to believe it may have been the QoT & LF behind this.
If LF thinks that the only thing that stands between him and the Rule of the Realm is Ser Kevan Lannister - we might have a very good idea what happened to Ser Kevan whilst travelling in the treacherous riverlands...
Ser Kevan's "vanishing" may well be the work of LF removing the one obstacle between him being named Hand of the King.
- so watch out Red Witch, the Spider is a much more capable plotter that Stannis' old Maester! If im right about this then it is going to be one great showdown!
