What is occurring on the atom level that causes grain boundaries, twin boundaries, and phase boundaries to exist?

Answer: Two dimensional and

three dimensional defects That is imperfections in the atom

Explanation: 2 dimensional and 3 dimensional defects which are imperfections especially in solids. This causes a high level of disorientation leading to grain boundaries, twin boundaries and phase boundaries.

In grain boundaries, There are different crystallographic orientation and it is a region of seperation between 2 grains or crystals.

In twin boundaries, there is a symmetry in disorientation which could be formed either by stress or annealing.