Pope Francis is coming to Canada soon to meet with aboriginal peoples about the RC church's role in the disastrous Residential School system. Doubt there will be any real "apology" offered - just a bunch of meaningless platitudes and vague promises.
But when you look at the long history of the RC church, you quickly see how such atrocities could and did occur. For instance, here's a great (and quite depressing) review of the incredibly cruel ways the church suppressed non-conformists across Europe over centuries . Now many of those people would have been Christians already, so it doesn't take much to see why they treated the native populations in the Americas as lesser being and heretics.