We get staining from the space balls. Maple and white oak seem to get it the worst. We don't do much natural, so the oil based stain washes out the oil from the space balls.
We use 1/4" balls, and make the panel a 1/4" less than the opening. As in, a 12" rail gets a 11-3/4" wide panel. Reading this makes me wonder if we should do 3/8" less than the opening. Once in a while we'll get doors that don't go together nicely, and squishing them less would probably reduce the oil getting squeezed out.