When i try to automate crafting an item that require any of the infusion stones from magical crops with durability. The AE auto crafting system will try to craft a new infusion stone instead of using the one in my inventory which still have durability available.

As far as I know this is caused by the fact that the infusion stones store their durability in the item's NBT data.

that is an issue on magical crops, if they implement the proper damage value, AE can take account for that

I don't think AE completely takes damage values in account; recipes with AE2 cutting knives have the same problem... Unless that was fixed recently. I haven't played a 1.7.10 pack in a few months.

You can make the recipe use substitutions, which will remove the durability requirement, but the recipe assumes the item is used up. If you have 1 on hand and request 16 crafts, it will think it need 15 more infusion stones.

If I recall correctly, the final infusion stone is never used up and works for all levels, and AE should know how to use that properly.