To reproduce: Put a stack of items on your hotbar, drop one of them on the ground right by your feet and right-click a beacon, villager or open any other GUI before picking up the item. Then watch the item pickup animation not play on your hotbar (the one that's shown even without having an inventory open, not the one in your inventory) as the stack size increases. Note that the held item moves up and down a second time once you close the GUI, this is likely related/caused by the core issue.

If you do the same with your regular inventory instead of a GUI the item pickup animation will play as expected.