Your problem with the pot appears to be a disagreement between where you think the pins in breadboard are and the pin numbers in schematic. If you select the two green wires on the pot in breadboard and right click and delete wire you will find that the rats nest is in fact the opposite direction to how you have the connections made. While it will let you make the connections you have it also then made a short (and the phantom rats nest lines) between the two pins of the pot which isn't what you want. It also now appears to remember the rats nest wires (which is likely a bug) so that the rats nest is still incorrect. Presumably that is why the duplicate / replace fixes the problem. If from your initial sketch, you delete the two green wires on the pot and then make the connections in breadboard following the rats nest connections (which will be a different physical layout than your current setup) the phantom rats nest lines will go away. I assume (but haven't checked) the other problems have a similar cure. Connections made in on view reflect in to the other two views so a mistake in one view can cause odd problems like this.
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