The California Indians lived off the land and had a very unregimented life, so the biggest shocks to them after moving into a mission were: 1) life was very regimented - you got up in the moring at a fixed hour, ate breakfast lunch and dinner at a fixed hour, attended mass etc. on a schedule that was uniform for all of the missions 2) you had to master a new language (Spanish, of course) and 3) you were quite busy working and didn't have the freedom you were used to...to wander into the woods on a nice day or go fishing.
Most of the Indians adjusted to this new way of life but some percentage - estimated at about 10-15% - became "run-a-ways." The Indians were given material things like clothing and blankets, their food became much more dependable and varied, and they received extensive instruction in the Catholic religion.
Discipline was strict (much like it was on sailing vessels of the period) and Indians who seriously broke the rules were punished, and sometimes whipped for a really serious offense. Most of the missionaries treated the Indians as "their children" and were quite solicitous of their welfare. The most troublesome offenses against the Indians were not perpetrated by the missionaries but by the 4-5 soldiersstationed at the mission, who could sometimes be quite cruel.