Those invisible cargo bays are the circuit connectors. It is correct, that they show up with count 0 when copying.
What is not correct, is that they remain after the cargo bay has been removed.
Can you give me the steps to reproduce this?
It looks like this is in a Blueprint sandbox mod, is it Factorio 2.0?
It's in 2.1. Happens when I'm pasting a bunch of cargo bays together using Shift. So if I have one row of 4 cargo bays, if I want to paste them in any direction the circuit connector are pasted 2 times. When u're pasting it, if u do it slowly u can see/hear the connectors getting pasted