Feeder adds unwanted hatches to category

You're saying it selected all the food options for stone hatch when you selected only ores for smooth hatch?
Because it is correct behavior that ores are checked in both categories.
 

If you chose a food source, say, phosporite, all critters able to eat that particular food source will be selected, whether they are shine bugs, hatches, etc.  

Thus, when you selected a particular food for stone hatches, all hatches that are able to eat that food will be able to use the feeder.  You can not chose a feeder to only feed a particular critter -- you can only chose it to dispense a particular food.

I'm not sure if that made sense.