Are the indigenous peoples of Ecuador Incas? Well, yes and no.
Although the tale of Juan Pizarro’s conquest of the Incas is set partly in Ecuador—Atahualpa, “the” Inca ruled from Quito and was engaged in a civil war with Huáscar, his half brother in Cusco—the peoples of Ecuador were mostly conquered by the Incas.
According to historian and ethnologist Frank Salomon, the non-Inca peoples suffered a fate similar to the Incas, whereby they lost much of their identity:
From the Cañari side, the attack on Cañari ancestors [by way of grave robbing] may have set into motion a process that the Inca state would not have allowed even if Cañaris had desired it, namely, the retrospective grafting of Cañari genealogy onto Inca descent. In order to understand how it occurred, one must remember that in Quechua [the common linguistic group of both peoples] thinking a dead person is considered to be present and active so long as he or she has physical existence. When the Cañari dead were taken from their tombs and exposed, broken and impoverished, they ceased to be rich, honored, and potent ancestors, and became dishonored, defeated, and disinherited ones. Neglected pre-Columbian ancestor mummies (gentiles) today form a class of hungry ghosts who pervasively haunt Quechua folklore in various regions. When the Spanish vandalized the Cañari dead and disposed of their bodies as garbage, they created a new common condition for Inca and non-Inca peoples alike, that of descendants of destroyed persons.
So the Cañari and some other conquered Ecuadorian people share a common fate with their Inca conquerors. Both are descended from “discarded” ancestors, so they feel a bond of sympathy with the Incas, who were primarily Peruvian.