Setting new ItemMeta of a Item entity's ItemStack fails if the block when the ItemStack is placed has an inventory (has block_entity_data), and instead writes a duplicate of the PDC into the item's block_entity_data.

See this paste, line 48-57. (In this example, the goal is to prevent items dropped on-death from despawning. The bug can be observed using /data get after using /kill holding a chest and picking it back up, or on line 56 where the ItemMeta should have been set to one without the key but retains it.)

The bug has been observed on shulkers, chests and hoppers, and does not happen on swords, grass, and trap doors.