Whenever I load my saved game, one of the automation wires is disconnected, even though I've connected it several times. As far as I can tell, this only affects wire built on the farthest left tile, which must be built fairly high in order to get above the neutronium.
Additionally, sometimes it still looks like it's connected, even though it's not:
Other times it will show it as being disconnected (as if I never dragged the wire with the mouse between the two) when loading. You can truly reconnect it by clicking and dragging wire over it, but it's a hassle to remember to do this every time you load the game.
Start a new game, dig & build ladders to the upper-left corner of the map, and place something with an automation port (e.g. bunker door) on the farthest-left square possible, above the neutronium. Send a green signal to the port (to make viewing the problem easier), then save and reload. The wire will be physically disconnected from the automation circuit, and may or may not look graphically disconnected as well.