Rich internal patch structure versus relatively simple, uniform patches. The matrix in which fragments are embedded may harbor activities and produce byproducts that are a direct threat to the patches that remain, while the threats from patch exteriors to natural fragments is less severe. Another, less obvious, consequence of fragmentation is that typically the size of fragments becomes increasingly skewed as habitat destruction proceeds. Loss of species doesn't occur until a significant fraction of the habitat has been lost. Once species begin to be lost from the system, they are lost very rapidly.
Halting fragmentation is always worthwhile if it is feasible.