More of a dummy dum-dum thing, but I was clicking items that fell with left-click for a while, assuming I was collecting them to put into an inventory, and got confused when I couldn't actually find an inventory to try to use the merging mechanic. Thought the recipe book was where you merge, but that wasn't it either, so I gave up on that. Didn't figure out that you right click items to pick them up until I right-clicked Byte to pick her up and the game registered me picking up some item instead.
Maybe deleted items can get a little puff of smoke effect? Or they explode? Or they do some effect where they fade into 1s and 0s?
Also kinda related: the purple orb item glows the same color as the "you can merge this" glow.