I looked for this as an existing issue but couldn't find it, though I was surprised as it happens to me constantly.

Often times if I have more than 2 stacks of something and one runs out, the mod will trip itself up trying to replace the item in my bar. It successfully replaces it, but then another stack goes into your inventory "hand". At first you don't notice anything weird, but then if you open your inventory, you'll be holding the stack as if you picked it up out of a slot to move it. Many times this causes the player to throw the stack on the ground if you use your hand, such as right clicking something. Just now I was setting up some laser drills, I placed a tesseract, it got refilled by the mod, then I went to right click the tesseract I placed and I threw another one into the laser beam destroying it. It's really frustrating.

Does this happen under the current branch or by any chances, under an older release?

I was playing on Infinity, which used InventoryTweaks-1.59-dev-152.jar

I thought so, digging into the archive reveals it is this cf6e263-commit. (Note that is is from 1. Aug 2014)
This begs the question if it is still in the codebase as is or rather in just older releases.
I might mess around with FTB Unstable 1.8.9 and see if I get InvTweaks to run and see if it still persists.

This problem still exists and has been around a loonnnggg time. I've experienced it with multiple versions of Minecraft, and just recently started testing 1.10.2, and Inventory Tweaks still has this problem. Exactly as Tesserex described, if you have more than 2 stacks of any given item (whether it stacks or not doesn't matter, you just need 3+ inventory spaces taken up of a single item type), it will refill your hotbar with the first stack, then put the 2nd stack into your "hand" slot. You don't even know it's happened 'till you open your inventory and see it already on your cursor. Occasionally with tools, it will also fail to update that it equipped a new tool in your hotbar, and even not let you mine things 'till you click the slot on your hotbar once. Not sure if is a different bug despite both happening at the same time. But I figured I'd mention it.

The most annoying aspect of this for me, is when you're mining, break a pick, have an extra equip on your hotbar, so you continue mining a while, suddenly realize your inventory is full, so you open it to look, only to find one of your extra picks is now stuck on your cursor and you're unable to put it into your inventory because there's no space. If you close your inventory now you auto throw it wherever you happened to be looking, so you have to make a decision right then and there which item slot to free up and which to throw.

Edit: Also willing to post pics/vids of the bug in action, or anything else that may help with this being reproduced and/or fixed. Just say the word.

This is still an issue as of 1.61.58.

Auto-refill is a nice feature but I simply have to turn it off because winding up with stuff floating on my cursor so often results in stuff being dropped.

Just threw a packed up drawer into the void ... FTB Skyblock (1.2.0 for mc 1.7.10). Gonna have to switch it off too, then.

This is happening with 1.9 as well. Using InventoryTweaks-1.61-dev-45.jar

Still having this issue in 1.63 with the addition of the item it actually replaces it with becoming invisible until it's placed or the inventory slot is clicked on. This is on multiplayer by the way, even with the server-side help enabled.

Same issue in MC 1.8.9. Auto refill turning off helps.

still an issue in 1.12.2

Nearly 3 years later, still happening and no dev response?