The bug
Clicking on a recipe continues to add the ingredients in the crafting grid as long as you have the items in your inventory even if the stacks in the crafting grid reached the maximum stack size. For items with a maximum stack size of 64 the additional items are placed in free crafting grid slots invalidating the recipe. For items with a lower maximum stack size the additional item is deleted.
How to reproduce
Put at least 16 + 1 ender pearls in your inventory
Put at least 17 blaze powder in your inventory
Open the recipe book
Shift click one the "Eye of Ender" recipe
Click on the "Eye of Ender" recipe again
→ One ender pearl is removed from your inventory but does not appear in the crafting grid, additionally one blaze powder item is placed separately in the crafting grid
The main problem seems to be that ingredients are added even if one or more stacks in the crafting grid already reached the maximum stack size. For items with a maximum stack size of 64 the additional item is placed in the crafting grid invalidating the recipe but for items with a lower maximum the item is deleted instead like you described.
Therefore I would like to make the report more generic, I hope you are fine with that.