Somewhat related to #19:
I use gulp-useref for my minification but as I understand, this is an issue of useref itself.
When using conditional comments like these:
<!-- build:css resources/css/main.css -->
<!--[if gte IE 9]><!-->
<link rel="stylesheet" href="./main.css">
<!--<![endif]-->
<!-- endbuild -->
Then the comment itself is being removed and becomes:
<!--[if gte IE 9]>
<link rel="stylesheet" href="resources/css/main.css">
<![endif]-->
This syntax is a valid syntax and usually used to load files for certain IEs and all other browsers (see Wikipedia)