I've never framed marbles, but now that you mention it, I want to try these possible mounting methods:
1. Make sleeves of clear polyester film, just slightly larger than the marbles. The sleeve could be quickly and easily fashioned out of a strip of clear film, perhaps 3" wide, with its edges creased lengthwise and poked through long slots in the mount board. You could make several sleeves of different diameters if necessary, and they could be placed vertically, horizontally, or at odd angles. For removal of the marbles, plug the ends of the sleeves with something -- maybe a cotton ball or a cork? The frame lid could open, allowing the marbles to come out one end of the sleeves when the frame is tilted.
2. Another method would be to make a "nest" for each marble in a matboard background and hold them in place with regular glass. Acrylic or coated glass, such as UV filtering or anti-reflection, would be scratched by the marbles. Or maybe glass would scratch the marbles...?
3. If the frame is not too large -- say, no bigger than 12" square -- a third method might be to cut perfectly round holes in a piece of clear film, about 25% smaller than the marbles' diameter, and rig the sheet in a strainer to hold the marbles from above. That would be like transparent nests cut into the clear film.
Whatever works, this would be a fun project to display in the shop, to demonstrate how versatile framing can be for hobby collections.