Program: 23180
Project: 23180
Buggy source:
@Override public Bundle loadBundle(InputStream stream,boolean isJson) throws FHIRException, IOException {
  Resource r2=null;
  if (isJson)   r2=new JsonParser().parse(stream);
 else   r2=new XmlParser().parse(stream);
  org.hl7.fhir.r4.model.Resource r4=new VersionConvertor_10_40(this).convertResource(r2);
  Bundle b;
  if (r4 instanceof Bundle)   b=(Bundle)r4;
 else {
    b=new Bundle();
    b.setId(UUID.randomUUID().toString().toLowerCase());
    b.setType(BundleType.COLLECTION);
    b.addEntry().setResource(r4).setFullUrl(r4 instanceof MetadataResource ? ((MetadataResource)r4).getUrl() : null);
  }
  for (  CodeSystem cs : cslist) {
    BundleEntryComponent be=b.addEntry();
    be.setFullUrl(cs.getUrl());
    be.setResource(cs);
  }
  if (killPrimitives) {
    List<BundleEntryComponent> remove=new ArrayList<BundleEntryComponent>();
    for (    BundleEntryComponent be : b.getEntry()) {
      if (be.hasResource() && be.getResource() instanceof StructureDefinition) {
        StructureDefinition sd=(StructureDefinition)be.getResource();
        if (sd.getKind() == StructureDefinitionKind.PRIMITIVETYPE)         remove.add(be);
      }
    }
    b.getEntry().removeAll(remove);
  }
  if (patchUrls) {
    for (    BundleEntryComponent be : b.getEntry()) {
      if (be.hasResource() && be.getResource() instanceof StructureDefinition) {
        StructureDefinition sd=(StructureDefinition)be.getResource();
        sd.setUrl(sd.getUrl().replace("String_Node_Str","String_Node_Str"));
        sd.addExtension().setUrl("String_Node_Str").setValue(new UriType("String_Node_Str"));
      }
    }
  }
  return b;
}

Fixed version (ground truth):
@Override public Bundle loadBundle(InputStream stream,boolean isJson) throws FHIRException, IOException {
  Resource r2=null;
  if (isJson)   r2=new JsonParser().parse(stream);
 else   r2=new XmlParser().parse(stream);
  org.hl7.fhir.r4.model.Resource r4=new VersionConvertor_10_40(this).convertResource(r2);
  Bundle b;
  if (r4 instanceof Bundle)   b=(Bundle)r4;
 else {
    b=new Bundle();
    b.setId(UUID.randomUUID().toString().toLowerCase());
    b.setType(BundleType.COLLECTION);
    b.addEntry().setResource(r4).setFullUrl(r4 instanceof MetadataResource ? ((MetadataResource)r4).getUrl() : null);
  }
  for (  CodeSystem cs : cslist) {
    BundleEntryComponent be=b.addEntry();
    be.setFullUrl(cs.getUrl());
    be.setResource(cs);
  }
  cslist.clear();
  if (killPrimitives) {
    List<BundleEntryComponent> remove=new ArrayList<BundleEntryComponent>();
    for (    BundleEntryComponent be : b.getEntry()) {
      if (be.hasResource() && be.getResource() instanceof StructureDefinition) {
        StructureDefinition sd=(StructureDefinition)be.getResource();
        if (sd.getKind() == StructureDefinitionKind.PRIMITIVETYPE)         remove.add(be);
      }
    }
    b.getEntry().removeAll(remove);
  }
  if (patchUrls) {
    for (    BundleEntryComponent be : b.getEntry()) {
      if (be.hasResource() && be.getResource() instanceof StructureDefinition) {
        StructureDefinition sd=(StructureDefinition)be.getResource();
        sd.setUrl(sd.getUrl().replace("String_Node_Str","String_Node_Str"));
        sd.addExtension().setUrl("String_Node_Str").setValue(new UriType("String_Node_Str"));
      }
    }
  }
  return b;
}