At first I thought this was an Extended Crafting issue or a mod pack related issue, hence this DarkPacks/SevTech-Ages#1649

But for some reason it occurred again with Immersive Engineering metal presses, here's another video of it voiding, iron ingots going into a metal press, it happens for some reason only when the translocators are next to each other.

https://streamable.com/3xqre

Can confirm, translocator deletes items when inserting into metal press due to metal press only accepting limited numbers and/or fixed stack-sizes depending on the installed press mold.