there really isn't a problem with calling this compute multiple times

src/compute_coord_atom.cpp

@@ -158,12 +158,6 @@ void ComputeCoordAtom::init()
   neighbor->requests[irequest]->half = 0;
   neighbor->requests[irequest]->full = 1;
   neighbor->requests[irequest]->occasional = 1;
-
-  int count = 0;
-  for (int i = 0; i < modify->ncompute; i++)
-    if (strcmp(modify->compute[i]->style,"coord/atom") == 0) count++;
-  if (count > 1 && comm->me == 0)
-    error->warning(FLERR,"More than one compute coord/atom");
 }
 
 /* ---------------------------------------------------------------------- */