Item entities turn invisible when dropped on the ground. The problem is intermittent, and I haven't found a way to reliably reproduce it. It doesn't seem to matter where the item entity comes from.
I've had items turn invisible both when tossing them out of my inventory and when being dropped from broken blocks.
It doesn't seem to matter what the item is. I've had it happen with seeds, lily pads and shulker boxes. The shulker boxes are especially worrying, because one invisible shulker box can result in the loss of a lot of valuable materials.