This must be fixed in today's build.
The boolean example does show a bug. I'll post here when it's fixed.
It's probably because you're describing your input B (the grids) as solid. Objects representing solids are OK to have boundaries (as grids do) so long as those boundaries do not come in intersection with the solid itself or the opposing geometry passed to Boolean. In other words, surfaces with boundaries can be treated like pieces of a solid parts of which is unknown, but only as long as the unknown parts (which start at the boundaries) are kept out of the operation.
However, in the case of the shatter operation, when generating only pieces of A, the result is the same whether B is marked a solid or a surface. If you change B to a surface, the warnings should likely go away.