Well you have the Incident at the village that set off the powder keg of tensions stemming from the elves refusing to help stop the darkspawn and general religious tensions, and started the war between Orlais and the dales which went much better for the elves then the humans at first.
In fact the elves apparently had aggressively and quickly overrun half Orlais and sacked a number of cities including the capital at the beginning of the war before losing their momentum by stretching themselves too thin about the time the chantry got around to declaring holy war on the elves after which the elves got nailed by a religious remotivated enemy, a sizable number of whom had their homes sacked and burned by the elves.
This still leaves me wondering what happened to get two groups of people who were previously allies to abandon that sentiment. Going from "lets rally against Tevinter" to "fight the darkspawn on your own" is a pretty big leap.
A long time and a lot of political ill between between neighbouring countries. As to the religious bit, well, there was a reason the Chantry expunged references to Shartan.
They removed Shartan's name after the the exalted marches as a means to justify what they had done. Resentment of the elves after they refused to help during the blight is understandable but an exalted march seems like a bit much. Really it just reenforces my belief that neither the elves or humans are as marvellous as they'd like to think.