The correct difference between the encomienda system and the repartimiento system of Spanish colonial America is that the encomienda system gave Spanish colonists control over Indigenous people in a specific area.
In contrast, the repartimiento system reformed the encomienda system by requiring that Indigenous people be paid a wage for their labor and limiting the amount of time they could be forced to work for Spanish colonists. The encomienda system functioned more like a grant of labor, while the repartimiento system aimed to provide certain protections to Indigenous people, albeit still exploitative in nature.