Here's what I would try...
"I received the shorts today, thank you for such timely shipping. Unfortunately, the blue pair has a hole in the back and a large stain on the front, while the pink pair has a hole in the front. Your auction stated some piling and fading and a small spot or two but didn't say anything about holes."
Now, do you want to keep all of them? Just the other two? What I'd say next would depend on what you'd like to do... Of course, if you want to return just two for a partial refund, it probably won't be worth it, because of shipping costs.
"Had I known about the holes, I probably wouldn't have bid."
Or you can just leave neutral fb-- "2 of 4 items arrived with holes not mentioned in auction." I've had people do that to me. On one occassion, she said one pair of shorts was a large, and it was definitely a small, I wouldn't have sold them to her as a small if they weren't. My other neutral was a Hard Rock Cafe t-shirt, which I sold as vintage ('87), and stated in the auction that it had some definite wear but lots of life left. They buyer said it came with stains! She never contacted me to say anything, just left neutral. I had second thoughts about selling that shirt, but I hadn't worn it in years...
Anyhow, retalitory feedback is against the rules. She can't leave you a neg if you did everything by the rules, and if she does, you can contact ebay to have it changed.