I have a Medium Assembler 2 building Yield Module 2 Boxes. Feeding it is a Small Demand Chest 1 via Inserter 3. Inserter 3 will not grab the 2 ingredients (Efficiency module 2 box and Yield module 1 box). I upgraded to Inserter 4 and that works. I double checked the inserter didn't have a 3rd random ingredient.

Do you have any other mods that affect things like stack inserter bonus, stack size, etc? I've tried setting up the system you describe and am unable to reproduce the problem. Though I've heard of similar things happening when stack inserters have a higher inserter capacity than the stack size of the items.

Did you ever manually insert materials into the machine? If something is overloaded sometimes an inserter can get stuck trying to insert the thing that's overloaded and is thus unable to insert other ingredients.

If you have a save that demonstrates it not loading something it should, I might be able to figure it out. But as of right now I can't see it doing what you describe.