The spontaneous formation of domains of commensurate vortex patterns near rational fractional matching fields of a periodic pinning array has been investigated with high resolution scanning Hall probe microscopy. We show that domain formation is promoted due to the efficient incorporation of mismatched excess vortices and vacancies at the corners of domain walls, which outweighs the energetic cost of creating them. Molecular dynamics simulations with a generic pinning potential reveal that domains are formed only when vortex-vortex interactions are long range.