A couple examples I've found so far...

Gas tank GUI: Shift-clicking a tank in the "-" slot moves it to the + slot instead of the player inventory.

Chemical Infuser GUI: Shift-clicking a gas tank in your inventory moves it to the left-most "-" slot regardless of the tank's content type or quantity. Especially bad since input slots come before output slot and C. Infuser does not check type of gas before moving it into its buffer and has no way to remove gases from its input tanks. (I've gotten the Hydrogen Chloride I'm trying to extract into a tank stuffed back into its inputs and had to "CLR" it multiple times already, even knowing about this - shift-clicking is such a habit! :D The only workaround I can find is to place empty tanks in the input slots to avoid accidents. And this is how I discovered #1555)

The gas tank behavior is intended.
As for the Chemical Infuser issue, it should be sorted out now that I fixed the buffer merge :)