// check first if both arrays have the same number of entries
if (input_array_size(value1) == input_array_size(value2)) 
{
  for (int i = 0; i < input_array_size(value1); ++i)
  {
    // At this point, your code has a problem, because you use "index" instead of "i".
    // The second parameter in the functions input_array_index/input_array_value
    // must not exceed the size of the array (i.e. the number of entries of the array) 
    // Otherwise you'll get an assertion failure.                                                             
    int    index_of_ith_entry_in_value1 = input_array_index(value1, i); 
    double value_of_ith_entry_in_value1 = input_array_value(value1, i); 
    int    index_of_ith_entry_in_value2 = input_array_index(value2, i); 
    double value_of_ith_entry_in_value2 = input_array_value(value2, i); 

    // eventually, you want to check if the indices are the same
    if (index_of_ith_entry_in_value1 == index_of_ith_entry_in_value2)
    {
      if (condition_valid(value_of_ith_entry_in_value2, gate, index_of_ith_entry_in_value1))
      {
        fill_output_array(GatedValue, index_of_ith_entry_in_value2, value_of_ith_entry_in_value1)
      }
    }
  }
}