Some mods do not add their mod items to the drop list in the LivingDropsEvent. This means that while the factory is learning they throw stuff on the ground.

So far I've seens reports, and confirmed from the code that:
RFTools, Actually Additions and ArmorPlus do this.

Possibly add a "hoover" feature to any learning factory that will check the surrounding blocks for items and grab/delete them. Not sure I can learn from these dropped items as people could cheat by dropping items near the factory.

I've tried a simple EntityItem check in the area around the factory when the factory is learning. I can capture and remove the drops, I can also learn them. eg. I'm seeing WitherBonesx6 from ArmorPlus. The only unfortunate thing is that you can see the item briefly.

The code just needs tidied up to now constantly create the AxisAlignedBB.