Procedure to make this bug happen.
1: Make sure your craft is made as shown on the image (you need to set is as the main unit)
2: Take the part that is attached to the rocket.
3: Drag it around.
4: Make sure this happens:
"The part that it's attached, and all the parts attached to that part, would duplicate and have the command chip attached horizontaly to the duplicated craft"
See the images if you don't understand what happens.
Thanks for fix this! @AndrewGarrison