In LIRGenerator::do_StoreIndexed():
    if (needs_flattened_array_store_check(x)) {
      // Check if we indeed have a flattened array
      index.load_item();
      slow_path = new StoreFlattenedArrayStub(array.result(), index.result(), value.result(), state_for(x));
      check_flattened_array(array.result(), value.result(), slow_path);
      set_in_conditional_code(true);
    } else if (needs_null_free_array_store_check(x)) {
      CodeEmitInfo* info = new CodeEmitInfo(range_check_info);
      check_null_free_array(array, value, info);
    }

Shouldn't it be:
if (needs_flattened_array_store_check(x)) {
}
if (needs_null_free_array_store_check(x)) {
}

If needs_flattened_array_store_check(x) is true then we emit a flattened array check. If the array is not flat at runtime then we fall thru and there's no check for a null free array.
But the array could be not flat and null free.