This can be reproduced pretty easily with a 1-length conveyor, an inserter, and a chest full of items. Place the inserter such that it takes items out of the chest and puts them in the conveyor. Then, place two stacks of items in the chest--say, iron ore and iron ingots. The conveyor will place the iron ore, then place the iron ingots--which will vanish into thin air.
Edit: It appears that the combined total of items needs to be less than or equal to a full stack, which suggests that the mod is checking to see if the resulting pile of items would be more than a stack, but isn't checking that the items are of the same kind.
This can be reproduced pretty easily with a 1-length conveyor, an inserter, and a chest full of items. Place the inserter such that it takes items out of the chest and puts them in the conveyor. Then, place two stacks of items in the chest--say, iron ore and iron ingots. The conveyor will place the iron ore, then place the iron ingots--which will vanish into thin air.
Edit: It appears that the combined total of items needs to be less than or equal to a full stack, which suggests that the mod is checking to see if the resulting pile of items would be more than a stack, but isn't checking that the items are of the same kind.