I have a mesh with tiny tunnels. I've noticed if their diameter is less than 4 times the voxel spacing, they are looked over.
This only happens for signed distance fields, and using the flag DISABLE_INTERSECTING_VOXEL_REMOVAL shows they are not skipped over but have wrong values and are then deleted.
My only workaround is to sample at a finer resolution and then downsample the grid. This however is much slower and memory intensive.
I've attached an example mesh, small_tunnel.stl, which is a tunnel of diameter 0.03. Sampling over a grid with spacing 0.01 shows the missing tunnel (in the screenshot I removed an outer wall to see inside).