How to remove section of a String containing a special character Java

I have a string

"apples, pears # and bananas\\ngrapes\\nbananas !apples"

I want to remove the string substring # and bananas.

private static String cleaned(String main, String substring) {
    return main.replace(substring, "");
}

but replace method doesn't work somehow. I feel it has something to do with the # because if I try getting the index of # using main.indexOf("#") i get -1.

When I call the method directly like this

System.out.println(cleaned("apples, pears # and bananas\\ngrapes\\nbananas !apples", "# and bananas"));

it surprisingly works I get the correct answer **apples, pears \ngrapes\nbananas !apples**. However when I call the method programmatically from another method like this

public static String stripComments(String text, String[] commentSymbols) 
    //some code
    return cleaned(stringBuilder.toString(), textAfterComment.toString());
}

it does not produce the correct answer. I get **apples, pears and bananas\ngrapes\nbananas**

Why do I get -1 meaning that # is not found yet it is clearly in the string? And how can I remove the substring with or without the replace method ?