If you include content in the custom CSS, e.g., to put a fancy open and closing quotes (U+f10d/U+f10e) on blockquotes, using backslash to escape the Unicode value, then the Theme Options page strips off the backslash in the Custom CSS. Therefore when you save the options (I think any option change not just Custom CSS), the character is not translated and the unescaped Unicode value appears in the rendered output.
Yes, this is the default behavior of Counsel Theme. If you can then reply with the code that you want to insert into Custom CSS. So that we will see how that can be implemented with the current stripslash behavior.