I suspect this applies to both Survival and Creative; when rapidly clicking in the enchantment table with an item, a graphical glitch occurs where the item appears to be duplicated (it is not). You can place the original item in your inventory but the one still in the table will disappear on clicking. You can hover over the item and it will display its name, and ID number if enabled. You can tell that this is a ghost item because the item cannot be enchanted as none of the sections are enabled, see picture.
Not a major bug, but still thought I'd report it.
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That's not the same thing I think;
Mine does happen in survival
It does not cause the item to delete, it merely creates a ghost of that item as well as letting you keep the old one
Spam-clicking items causes same effect. Can sometimes disappear even in survival, see MC-4108.
Duplicate of MC-341.