Different processes written by different people at different times might have different lists of inputs for no particular reasons... 
It really depends what "bad" is. If you are processing SEEG and you have half of your electrodes that were not plugged, you don't want to spend time computing complicated measures on empty signals.
Also, this concerns bad SEGMENTS. You may have periods where the subject is moving that you'd like to remove.
The configurations are infinite, we're trying to provide tools that can satisfy everybody, up to you to find what is the correct combination for your data.