i guess it's somewhat self explanatory:
When opening a gui, like the mechanical infuser and shift clicking some iron ingots the stack moves into the corresponding field. But instead of visually moving, one now has a ghost stack of the same size in his inventory. That one is removed a few seconds after the gui is closed. (if opening directly after one closed it, the ghost still seems to be "alive")

Yeah, honestly have no clue where to go with this desync. It's been occurring for years and I still haven't been able to find a fix.

why you don't label it as "unclear how to fix" or similar and/or maybe let it open?