Why can't we move our toes and some fingers separately?
A relatively new area of the brain's cerebral cortex evolved to enable humans and other primates the necessary small motor skills to pick up small objects and deftly use tools, scientists now say. https://www.youtube.com/watch?v=zyl6eoU-3Rg

Primates can move their ears too, here's a theory of it. Other motor skills that are not often developed are individual eyebrow movement, pectoral flexing, ability to sneeze with your eyes open.

Hand movement is new and developing compared to chimps. 

Toe movement is latent and receding. 

The human hand is built up onto a squirrel/clawed paw, If you take a while to rotate your forearm and the flexors of the fingers, you will see that it's a mutated simple flexing mitt thing with with a new fine motor dexterity that you use all day, added on top of the vestigial clawing and grasping hand.

https://www.youtube.com/watch?v=vlwAoKpSI7s

This page says: 
Signals generated in the primary motor cortex travel down the corticospinal tract  through the spinal white matter to synapse on interneurons and motor neurons in the spinal cords ventral horn. Ventral horn neurons in turn send their axons  out through the ventral roots to innervate individual muscle fibers.

The motor cortex is subject to plasticity and remapping. To know this question is beyond my field of knowledge, someone else can go on from here :) you'd have to learn about the motor cortex, plasticity, vestigial nerves, nerve mappings, it's a fantastically complex topic.

What's interesting is the variety and quantity of different muscular abilities that are inherited by a population, it reflects an optimized level of evolutionary plasticity and specific types of variety of useful traits like muscle and joint proportions to ensure fast and flexible species development.