I'm the same way. If its natural variation, its acceptable. If its a QC issue, than its unacceptable.
Personally, if it were me, I'd send them back. Even if a replacement was not available.
The part that irks me the most is that it almost seems like they try to sneak this kind of thing past us. Like when you negotiate a price with someone and they hand you the cash and its short $10 and they are just trying to see if you will accept it for less. Then when you point it out, they have a $10 bill in their back pocket all by itself with no other money, making it obvious what they were trying to do.
Its like: "here, we'll send him the stained shoes, see if he accepts them. That way we can get rid of them. If he complains we'll just act like we didn't notice it and say that we are more than willing to refund his money".
(Not directing this specifically at any retailer, just a general statement. Also, I know that the retailer can send defective merchandise back to alden and recoup their money, so its not like the retailer is stuck with them either. Not sure why or how this stuff happens, but I'm also not the first to wonder about such things)