Happened when a loop to same node from port se to ne was changed to port ne to n (because another edge had appeared at the East port and was crossing through this loop edge).
Input:

/* This is input to the "dot" or "WebDot" program, part of Graphviz */
digraph G {
    /* tester_run.ksh has a loop inside it */
    tester_run_ksh:ne -> tester_run_ksh:n ;

#    /* run this edge through an invisible point for a right angle around
#     * obstructing subgraph */
#    tester_run_ksh -> point1 [ constraint=false, arrowhead=none ];
#    point1 -> copy_summ_awk;

#    tester_run_ksh[label="tester_run.kshn(ends only upon error)"];
#    copy_summ_awk[label="copy_summ.awk"] ;

#    /* testing use of fontsize=0 to see if that makes it have no label */
#    point1[ shape=point, width="0.01", height="0.01", fontsize=0 ];


#    subgraph aligntune5{
#        rank=same;
#        tester_run_ksh;
#        point1;
#    }

}