Strip whitespace will remove all linebreaks, tabs en double spaces from your code.. and the tricky part is the linebreaks. Take a look at this piece of code.
//alert the user.
After strip whitespace the complete statement has become a comment, because you didn't close the comment.
<script>//alert the user. alert('Eeej!!');</script>
Correct way of having comments in your code is like this.
/* alert the user. */
This way the code won't break down when you use a whitespace removal script or tool. Also important in this manner is the use of the ; to close every line of code!!