Clone command randomly destroys blocks

Building a simple garage door that I have done a few times. One side of the circuit raises the door, other lowers it. For whatever reason, it will randomly erase lines of blocks. It says they are cloned, but they are nowhere to be found. I have checked all the coordinates and have seen no errors. Even removed all the block and started over to no avail. Any ideas?

On further inspection it is randomly reversing the order of the clone and fill blocks. I still have found no reason why.