The treatment of Indians at California missions is simply inhumane, brutal torture, simply blatant slavery. They were forced to do something they don't like. If they refused to work, they were deprived of food for one day, and if they were absent from church, they receive corporal punishment, which is plain harsh and hellish. They were converted to Christianity by force and coercion. If they resisted, they were severely punished from their defiance. There are reports of escapes during the missions, heightening the fact that the missions are like concentration camps.
The missions in California served as a Spanish base to both explore land and 'christianize ' Indians. The Spanish viewed their mission in a positive light and felt that their mission was a divine one. When the Indians came to the missions , often they were converted by force. It is easy to see how the cultural perspectives of what was happening in the missions diverged.
The Spanish padres and missionaries felt they were doing the necessary work of God, and that if the Indians resisted conversion or religious education, that punishment was necessary. Punishment was often physical, and brutal
From the perspective of the Indians, this establishment of the mission system was nothing less than the death of their culture, and a genocide of their people. They were forced to live and work at the missions, and often punished for resisteing, which would make it no better than slavery.
Hope this answer was helpful. The link below gives further information based on Native tribal records.