That I know of, the timeframe with Bryce and Eleanor and when they get married contradict the lore presented in the game. It also seems to go against their apparent ages in the game.
There is a similar contradiction with the city elf's father. And I think there was something about who was an elf leader at what time and who succeeded that elf. I'm not as familiar with this one though. My main Origins character is a Cousland, not an elf, so I'm more familiar with the first example.
It's unknown why she didn't have kids with Maferath until later. It may have had nothing to do with her physical ability to do so.
I've already noticed that the writers messed up a bit with the timelines, but that doesn't discredit all of the book.
Also, the idea that she was too weak to bear children is something that appeared in many texts.
No, darkspawn do not explain drought and flooding. Those are two contradicting events. If tunnels diverted water away, then they may get drought. Fine. But in that case they don't get flooding, because the water was redirected. The only way a flood occurs in that case is if it rains hard for a long period of time. Both of these are easily explained, and easily countered for mages of Tevinter. A drought is easy to explain. Either your rivers and lakes dried up, or you get no rain for long periods of time. But either way, the mages should have been able to replenish the water via magic. They couldn't. Why? The Maker. And it wasn't just lack of water. The Maker also burned the crops with intense heat. Then he sent massive rainfall to erode the soil. And this was widespread, not just in one area. So that is too much to be a coincidence or even darkspawn.
Okay, I'm not a meteorologist but I know that drought leads to favorable conditions for wildfires. Moreover, rain after drought is known to lead to floods because the parched ground is slow to absorb the rain. I don't know the exact season these events occurred but if it was winter time it's plausible to suffer from both famine & drought followed by flooding. It doesn't really prove nothing.
As said in the previous post, nothing is definite, they don't give enough evidence to prove/disprove the Maker.
Assuming Corypheus isn't lying, an empty throne doesn't mean the Maker doesn't exist. It just means the Maker wasn't sitting on the throne at the exact time when the magisters invaded the Golden City.
Caddius wrote it beautifully 
Just want to add that Corypheus consistently refers to 'the throne of the gods'. I'm guessing he's using that metaphorically, since I doubt seven Old Dragon Gods are going to share a single chair. And I doubt that there was a single chair.
Again, as the Inquisitor points out to Giselle, as deranged as Corypheus might be, he is an eyewitness to the Black City Assault, and his testimony is immeasurably more valuable than the Chant, which as people have been pointing out, has undergone massive revision and editing in its history, because the Chantry is an organization as human as any other.
Why is it slim? Tevinter attacked the Maker's house first, didn't it?
My point is that if the Maker were bringing the pain to Tevinter, then he started by sending their corruption back to the world with them. That was the counterattack. That's one heck of a wallop if you ask me. But then when Andraste joins the fight, then the Maker switches to other tactics so Andraste and her followers can take part as well.
She had to convince him not to give up on the world. Theoretically, the taint should have been enough to bring Tevinter down over time. So of course he's going to recommend she bail on that world just like he did. Then when she appealed to him, he decided to give the world another chance. Thus, the tactics changed to where Andraste would lead the charge in taking down Tevinter.
I think the Maker could control the minds of darkspawn sure. Not that he would need to. I'm not saying he intended to take down Tevinter with waterway diversions due to darkspawn tunneling, that was probably just how it worked out, IF the water really was diverted by the darkspawn. All I'm saying here is that the calamities that befell Tevinter, including the darkspawn, were the Maker's doing. So even these circumstances were because of the Maker.
First thing, I think it's slim because it wasn't spoken of anywhere and makes little sense with we know of the Maker.
Canticle of Silence 3 speaks of the Maker getting angry because the magisters breached the Golden City using the blood of innocence because they were power hungry. He didn't even seem to get mad that fact they entered him realm, just the way they did it and why.
The canticle didn't speak of vengeance, at the end when He throws the magisters back He was sorrowful more than angry.
"And the Maker in sorrow turned His gaze,
And no longer hoped for His children to return."
If His goal was to bring pain to Tevinter then He pretty much failed since most of the pain was felt by the poor dwarves.
The taint affects all of the Thedas, sending the magisters back with taint in hope it destroys the Imperium is pretty much giving up on His children.
There is another side affect to the darkspawn's tunneling:
As the darkspawn advances to the surface, the land around them is sucked out of moisture, bringing wasting force that blackens the earth and withers plants to dust.
The darkspawn resurfaced at -380 Ancient, at the edges of the Imperium, if this is really one of the side-affects of the darkspawn's presence then it compliments the drought even more.
I'm going by what the spirit in the temple said in DA:O. Now, if this were just a matter of strategy, I don't see why Maferath would betray Andraste. He would simply call a ceasefire, or make a deal with Hessarian to call a truce, and that would be it. But no, he gave Andraste over to Tevinter. Why? Jealousy is the only answer we have.
And we also learned that the elven pantheon is nothing but a bunch of spirit harboring mages.
If you speak about the spirit of Maferath, then know that there is more than one right answer, it could be jealousy or "I don't know".
But that's besides the point, he is a spirit, like Justinia V was a spirit in the fade, spirits are not complex beings. The spirit of Justinia just took her form and what is remembered of her, it could be the same for the spirit that imitated Maferath.
Maferath could've called ceasefire, sure, but then all of the sacrifices were for naught, and I doubt Andraste would've agreed for a ceasefire. Andraste was a threat, the Prophet of a new religion, for Hessarian getting rid of her is worth enough for truce.
Don't forget the two debated long and hard on the terms of their truce, perhaps it wasn't even obvious at first there was a need to sacrifice Andraste.
Maferath took with him his Aegis, and arrived at the appointed place
Where Hessarian waited with his guard, and the two leaders of the armies spoke,
Guarded in riddles, and came to an understanding between them
That peace bore a heavy price which must be paid in blood.
Also, we learned nothing of the Elven Pantheon, Solas said they could've been powerful mages, spirits or something else entirely. This doesn't negate the fact they were worshiped and were said to reside in the Beyond (which is the Fade).
Old elven beliefs call it "the Beyond", a holy place once home to their gods. What little of elven lore has survived speaks of Fen'Harel, a trickster god who schemed to take the Beyond for himself, imprisoning his brethren in the Eternal City at its heart. The elves believe their gods remain trapped in the prison to this day, as Fen'Harel, the Dread Wolf, gleefully patrols the Beyond to feast upon the souls of the dead.
We already have proof that some of the elven lore is correct, Fen'Harel exists, Mythal exists. The Golden City was thought by the elves to be the residence of their gods, we have nothing to contradict that.
The way I see it, they confirmed the Maker's existence in DA:O, and now that the series has taken off, they are trying to undo what they already proved in the first game in order to make the storyline more mysterious.
Where was it confirmed?