Invisible Vertical Gas Pipes:
When the gas stops pumping the underlying pipe disappears.
Phantom Gas Pipes:
When missing the Priority button and moving the mouse the game will automatically place what you want to build without holding the left mouse button. You have to press the left mouse button to get it to stop. When missing the Priority button aim between the list of numbers and different build icons and move the mouse.
As for the ghost image it appeared from that and wouldn't disappear until I reload the game. I used Cancel and Deconstruct to get rid of them, but couldn't. This is the only time its happened.
This is more of a design scroll bar movement miscalculation. When there's 6 or more materials listed to build with, that's the farthest it goes to the right, so you can't see all of the farthest right material.
Explained in main post.