Woah, that's definitely.. weird. It sounds like... I feel like there shouldn't ever be 2 reverse recipes for the same item, because the way I create these recipes, is to take an item from the list of all items (EG, Pycoal dust), look for it in the list of all recipes, and if there is an exact match, to create a reverse recipe for that item.
For items that can be produced in multiple methods (such as Angel's ores, or certain refining methods) the recipe is actually named something else internally, so they don't conflict with each other. These recipes are never looked at, because they don't match the internal name of the item.
The only way to have 2 different reverse recipes for the same item... I guess, if that item has 2 different recipes, with the same name? Like they might be made in different machines, and since they're from different mods, they might happen to share the same name. Although that is definitely weird...
So the mods in question would be Yuoki's, Angels, and PyCoal? Maybe Bobs? Any other compatibility mods I might need? Like there's definitely a few for PyCoal and Angels, and I think Yuoki's has a few mods that affect its tech tree.
So a list of any and all mods that might affect the coal dust items/recipes, and any mods that might alter those mods, would definitely help to narrow down the issue. A long term solution would probably require a bit of an engine tweak, very complex things. As for a simple solution... there's an easy way to disable the recipe entirely, but that wouldn't really help with the issue of Pycoal dust being useless.
Using stack inserters with stack size greater than 10, pulling from a box, and being disabled if the box has less than 10 coal dust would technically circumvent the issue, by ensuring there's never less than 10 coal dust being put in to the machine. Or if you don't mind it affecting recycling times, you can also increase the timer for Automatic Ingredient Push Delay (or whatever it was called, under Mod Settings), so your inserters have more time to input items before they get auto-ejected from the machine.