Program: 96872
Project: 96872
Buggy source:
public void flush(){
  sortMeshes();
  final int numFacesPerBatch=50000;
  int faceCountInBatch=0;
  Batcher batcher=SilenceEngine.graphics.getBatcher();
  Material originalMaterial=SilenceEngine.graphics.getCurrentMaterial();
  Texture originalTexture=Texture.CURRENT;
  Material material=meshes.get(0).getMaterial();
  material.getDiffuseMap().bind();
  SilenceEngine.graphics.useMaterial(material);
  Vector3 temp=Vector3.REUSABLE_STACK.pop();
  if (transform != null)   batcher.applyTransform(transform);
  batcher.begin();
{
    for (int i=0; i < meshes.size(); i++) {
      Mesh mesh=meshes.get(i);
      if (!mesh.getMaterial().equals(material) || faceCountInBatch > numFacesPerBatch) {
        batcher.end();
        material=mesh.getMaterial();
        material.getDiffuseMap().bind();
        SilenceEngine.graphics.useMaterial(material);
        if (transform != null)         batcher.applyTransform(transform);
        batcher.begin();
        faceCountInBatch=0;
      }
      Transform transform=transforms.get(i);
      Color color=mesh.getMaterial().getDiffuse();
      for (      Face face : mesh.getFaces()) {
        batcher.vertex(temp.set(mesh.getVertices().get((int)face.vertexIndex.x)).multiplySelf(transform.getMatrix()));
        batcher.normal(mesh.getNormals().get((int)face.normalIndex.x));
        batcher.texCoord(mesh.getTexcoords().get((int)face.texcoordIndex.x));
        batcher.color(color.x,color.y,color.z,mesh.getMaterial().getDissolve());
        batcher.vertex(temp.set(mesh.getVertices().get((int)face.vertexIndex.y)).multiplySelf(transform.getMatrix()));
        batcher.normal(mesh.getNormals().get((int)face.normalIndex.y));
        batcher.texCoord(mesh.getTexcoords().get((int)face.texcoordIndex.y));
        batcher.color(color.x,color.y,color.z,mesh.getMaterial().getDissolve());
        batcher.vertex(temp.set(mesh.getVertices().get((int)face.vertexIndex.z)).multiplySelf(transform.getMatrix()));
        batcher.normal(mesh.getNormals().get((int)face.normalIndex.z));
        batcher.texCoord(mesh.getTexcoords().get((int)face.texcoordIndex.z));
        batcher.color(color.x,color.y,color.z,mesh.getMaterial().getDissolve());
        faceCountInBatch++;
      }
    }
  }
  batcher.end();
  Vector3.REUSABLE_STACK.push(temp);
  originalTexture.bind();
  SilenceEngine.graphics.useMaterial(originalMaterial);
}

Fixed version (ground truth):
public void flush(){
  sortMeshes();
  final int numFacesPerBatch=50000;
  int faceCountInBatch=0;
  Batcher batcher=SilenceEngine.graphics.getBatcher();
  Material originalMaterial=SilenceEngine.graphics.getCurrentMaterial();
  Texture originalTexture=Texture.CURRENT;
  Material material=meshes.get(indices.get(0)).getMaterial();
  material.getDiffuseMap().bind();
  SilenceEngine.graphics.useMaterial(material);
  Vector3 temp=Vector3.REUSABLE_STACK.pop();
  if (transform != null)   batcher.applyTransform(transform);
  batcher.begin();
{
    for (    int i : indices) {
      Mesh mesh=meshes.get(i);
      if (!mesh.getMaterial().equals(material) || faceCountInBatch > numFacesPerBatch) {
        batcher.end();
        material=mesh.getMaterial();
        material.getDiffuseMap().bind();
        SilenceEngine.graphics.useMaterial(material);
        if (transform != null)         batcher.applyTransform(transform);
        batcher.begin();
        faceCountInBatch=0;
      }
      Transform transform=transforms.get(i);
      Color color=mesh.getMaterial().getDiffuse();
      for (      Face face : mesh.getFaces()) {
        batcher.vertex(temp.set(mesh.getVertices().get((int)face.vertexIndex.x)).multiplySelf(transform.getMatrix()));
        batcher.normal(mesh.getNormals().get((int)face.normalIndex.x));
        batcher.texCoord(mesh.getTexcoords().get((int)face.texcoordIndex.x));
        batcher.color(color.x,color.y,color.z,mesh.getMaterial().getDissolve());
        batcher.vertex(temp.set(mesh.getVertices().get((int)face.vertexIndex.y)).multiplySelf(transform.getMatrix()));
        batcher.normal(mesh.getNormals().get((int)face.normalIndex.y));
        batcher.texCoord(mesh.getTexcoords().get((int)face.texcoordIndex.y));
        batcher.color(color.x,color.y,color.z,mesh.getMaterial().getDissolve());
        batcher.vertex(temp.set(mesh.getVertices().get((int)face.vertexIndex.z)).multiplySelf(transform.getMatrix()));
        batcher.normal(mesh.getNormals().get((int)face.normalIndex.z));
        batcher.texCoord(mesh.getTexcoords().get((int)face.texcoordIndex.z));
        batcher.color(color.x,color.y,color.z,mesh.getMaterial().getDissolve());
        faceCountInBatch++;
      }
    }
  }
  batcher.end();
  Vector3.REUSABLE_STACK.push(temp);
  originalTexture.bind();
  SilenceEngine.graphics.useMaterial(originalMaterial);
  meshes.clear();
  transforms.clear();
  indices.clear();
}