Firstly, a quite large segment of the indigenous voters didn’t vote for the conservative candidate per se, but for the leading opponent to Correa. See for example the difference between the presidential and the national assemblymen’s elections in the Shuar- and Saraguro populated areas: in these places, indigenous voters voted for Lasso in the presidential poll but for Pachakutik, a fairly left-wing party, in the legislative election. I have already gave several reasons for why the indigenous voters dislikes Correa: the government’s support for mega-mining and oil drilling in indigenous-populated areas; Correa’s feud with the CONAIE, the main indigenous organization; crackdown on indigenous protests (remember that the province of Morona Santiago is under a state of emergency); modification of the water law in a sense that seems to favor big agro-business over small-scale farmers; Correa’s long-time refusal to comply with Pachakutik’s indigenist platform (transformation of Ecuador into a plurinational state; creation of an indigenous justice system; comprehensive agrarian reform; aggressive promotion of indigenous languages).
Ugh, that's incredibly disappointing. Thanks for the explanation though!
If you're interested in indigenous politics in Ecuador, I'd highly recommend "Crude Chronicles," by Suzana Sawyer.