Premis:
When requesting "Assembler Matrix Craft Core", the system shows "missing Items" while completely ignoring that a Substitution is available.

Detail:
I have the Recipe for a "Crafting Table" set to "Substitutions Enabled", when I then request said "Crafting Table" the System tellls me that I am missing "Oak Log" for more "Oak Planks" while I also have a recipe for "Dark Oak Planks".
The System also tells me that other usable "Planks" are available, but it does not register that it can make more of the Substitution.

Version:
ExtendedAE-1.21-2.2.15-neoforge.jar

It has nothing to do with ExtendedAE and substitutions mode. AE can't request different sub crafting tasks for the same item.
Even you have patterns like this: B->A, C->B, D->B. AE won't use both C and D to craft B at the same time.
You can send this request to AE's github issue if you want such feature