That is the issue. When the clear sequence runs, it uses Select Subject and expands the selection (which is why the areas become larger). Nothing inside of the expanded section will get cleared.
There isn’t really anything I can do about what Select subject does as that is all on the Photoshop side handling that. However, I have never seen Select Subject pick up weird little pieces of nothing like that. I’m not sure what it thinks those areas are to be part of the subject.
Can you send me the full res image… the exact image you are running through the batch. I’m curious to see if Select Subject does that on my computer for the same image or if your computer is behaving differently.