This was originally reported as an issue with JEI. It turns out that disabling Inventory-Tweaks fixes it. When a recipe is open, and the inventory UI is occluded, items being added cause a row of inventory to be deleted and duplicated from one below.

Original report: mezz/JustEnoughItems#156 (comment)

Inv Tweaks version: 1.60.beta-30
Forge Version: 11.15.1.1730

Even with the server module, Inventory Tweaks only ever causes the equivalent of a manual click. If things are setting duplicated, they are either client-side only glitches (which can tun into real items -- if you're in creative), or whatever outside code is handling the clicks is messing up.