How to Remove Ghost Duplicate Pins in Circuit Appearance
Unfortunately I don't have Logisim Evolution installed, but the last &quot;original&quot; Logisim, version 2.7.1. Opening the circuit led to an error message concerning 4 erroneous elements &quot;circ-port&quot;.
Anyway, the saved circuit is an XML file. And you can open it with any editor, but using a programmer's editor highlights the syntax, which is really helpful.
So I did, and looked in the circuit &quot;Register_Controller&quot;. Matching the list of &quot;circuit-ports&quot; of the &quot;appearance&quot; (lines 2837 to 2888) with the pins (lines 3031 to 3369) revealed that four of the circuit-ports have no pins in the circuit.
Deleting the lines 2846, 2848, 2850, and 2852 (and saving the file with a new name) made Logisim load the file without error message.
Here are the lines (with the not-to-be-deleted lines between them):
      &lt;circ-port height=&quot;10&quot; pin=&quot;190,330&quot; width=&quot;10&quot; x=&quot;75&quot; y=&quot;75&quot;/&gt;   &lt;!-- delete me --&gt;
      &lt;circ-port height=&quot;8&quot; pin=&quot;280,370&quot; width=&quot;8&quot; x=&quot;46&quot; y=&quot;136&quot;/&gt;
      &lt;circ-port height=&quot;8&quot; pin=&quot;190,380&quot; width=&quot;8&quot; x=&quot;46&quot; y=&quot;156&quot;/&gt;   &lt;!-- delete me --&gt;
      &lt;circ-port height=&quot;10&quot; pin=&quot;530,390&quot; width=&quot;10&quot; x=&quot;45&quot; y=&quot;185&quot;/&gt;
      &lt;circ-port height=&quot;10&quot; pin=&quot;190,400&quot; width=&quot;10&quot; x=&quot;75&quot; y=&quot;65&quot;/&gt;   &lt;!-- delete me --&gt;
      &lt;circ-port height=&quot;10&quot; pin=&quot;530,410&quot; width=&quot;10&quot; x=&quot;45&quot; y=&quot;195&quot;/&gt;
      &lt;circ-port height=&quot;10&quot; pin=&quot;190,420&quot; width=&quot;10&quot; x=&quot;65&quot; y=&quot;455&quot;/&gt;   &lt;!-- delete me --&gt;

After sorting the coordinates, I also found duplicates at the coordinates (200,330), (200,380), and (200,400). These are named NOT(NOT), Out (ROut), and Load (RIn), respectively.
However, I have no idea why Logisim Evolution produced this erroneous circuit. Presumably there is a bug in it. You might consider to report this at the project's site.