Can Bondo be used as a filler in plywood floor repair?

Not if your going to finish the floor. Now if your going to repair a spot and cover it over there are many floor patch products and floor leveling products that you might consider. But for crack filling and refinishing work I'd recommend "Woodwise" filler.

Hope this helps.

John

P.S. Just realized you were asking about plywood. I'd probably still would check into a wood patch product. Any hardware store should be able to address this for you.