I've only seen this happen consistently with the EnderIO crafter and specifically the pipe crafting recipe, where a second iron bar never arrives, so far. This only happens in the "per craft" and "all" insertion modes.

• Idea 1: I haven't managed to find a clear reason for this, but I assume it has something to do with the fact that, out of the many recipes I've tried, both pipes (the output) and iron bars (one of the inputs) are (one of) the only ones that have a high output amount - so maybe something gets confused there when calculating how many inputs are actually needed?
• Idea 2: Because the insertion mode that it doesn't happen with only differs in a travelingIngredients.isEmpty() check, maybe the traveling ingredients collection gets confused somehow?
• Idea 3: in store, getTravelingIngredient is used to shrink the traveling ingredient of the given type, but only a single traveling ingredient is ever compared against. Since the issue only happens with a second iron bar being delivered in the recipe, maybe the same iron bar ingredient gets deducted twice somehow or something

Reproduced this with multiple recipes, and it's always specifically the last item in a set of the same item missing (like when four redstone should be sent, it's 3 instead, etc.), and it's always fixable by switching to singles mode! I'm still not sure what exactly causes it though.