FIFA gave no timetable for a possible disciplinary case ahead of the World Cup kicking off Nov. 21.
Ecuador placed fourth in the 10-nation South American qualifying group to advance directly to Qatar. Fifth-place Peru has a playoff game next month against Australia or the United Arab Emirates.
Chile placed seventh, seven points behind Ecuador, but argues it could advance if games involving Castillo were forfeited.
The FIFA rules in cases of ineligible players require results to be overturned as a 3-0 loss.
Ecuador’s soccer federation issued a statement rejecting Chile’s claims and insisting that Castillo is legally an Ecuadorian citizen.
Chile has now filed complaints against an opponent’s player in back-to-back World Cup qualifying programs.
In South American qualifying for the 2018 World Cup, Bolivia forfeited two games in which it fielded an ineligible player as a late substitute. FIFA had received complaints from Chile and Peru about Bolivia defender Nelson Cabrera, who was born in Paraguay and had previously played for Paraguay’s national team.
Bolivia lost an appeal at the Court of Arbitration for Sport which said FIFA was right to investigate even when protests were filed weeks after the games were played. That case ultimately harmed Chile. Three extra points awarded to Peru lifted it above Chile to enter an intercontinental playoff that it won.