If you have a full inventory and you convert an item like iron blocks to iron ingots with a near stack of ingots in your inventory then it will try to go over 64 and anything converted past 64 is lost. This affects diamond, gold, iron, lapis, redstone, slime blocks, gold ingots to their smaller forms and also anything else that can be crafted which gives multiple items like slabs, pillared quartz etc.

The 2 attached photos show an easy way to reproduce.