I'm not entirely sure what to call it, but the bug is where you pick up an item, or put down an item, or place things in a crafting grid, or anything to do with moving items really, it will (in the engine) get placed down, or picked up, but VISUALLY, does not appear to have been placed down, or picked up. For example, you pick up a diamond, ghost it in a crafting grid, then go to put it down in your inventory. You see the shift of it being placed down, only instead of it staying where you put it, it's as though you hadn't put it down at all. But when you go to click where you wanted to put it, it gets picked up. This may be entirely a terrible description. :'C
I know exactly what you mean. I have a feeling it may be an issue with MouseTweaks or InvTweaks. This issue has persisted since 1.5.
If there were an agree button for a post, I'd put it on Flutter's post. Also, if it's that big of an issue, you can always choose to uninstall Mouse/InvTweaks from the launcher, however it's not a bug SKCraft could fix (as far as I know).
You can turn off a feature in the options menu for InvTweaks. It seems to help a little for me with regular inventory stuff, but it still happens in the crafting grid.