Setup:
Chest -> Itemduct -> Retriever -> Altare
Retriever is filtered for craftables, extraction rate 1, max stack size 1.

When adding Inert Blood Iron Ingots (Infused Blood Ingots) and Glowstone (Blood Infused Glowstone) to the chest, they are both piped to the Altare, the first to arrive is immediately started to craft and as soon as the second arrive, it appears and disappears a tick later in its inventory and the material is gone.
It looks similar to piping the same material into it slowly, like if you pipe 1 ingot in, it starts crafting, if you pipe a second in while crafting, it is added to the current crafting operation so the altar is crafting both.
I guess that the Altare tries to start the craft of the second item, doesn't see that it is currently crafting something else and then voids the second item as it assumes it was added to the current craft.

Feature suggestion / fix: When a craft is in progress, never add to it. This allows you to pipe slowly (slow itemducts, hoppers etc.) and craft 1 at a time instead of having to wait on full stacks to craft.
This allows you to control the amount crafted at once by changing the pipe rate, i.e. with Servos/Retrievers from Thermal Expansion, you could set the rate of transfer to 10, then it will take up to 10 items of 1 type at a time and transfer in one operation, then the Altare sees that it has a craftable stack of 10 and begins crafting, if anything else arrives, even if it is the same material, it is ignored until the craft completes and then the next stack of however many there are, is started.
This would work great with a lot of mods that allow setting a limit to the amount that is stored in the inventory of the Altare, e.g. if a Retriever is set to "Keep 10 in stock" and "Extraction rate 10", then the Altare will always craft 10 at a time, whereas now, it sees it got another 10 and it just adds them to the current craft until a full stack is crafting.

Sorry for the confusing descriptions.