Typically during the VIF, we mark those kinds of things up and we always take good pictures. The words I use are, "the VIF is to cover any concerns you (the customer) may have, as well as document any concerns that I have that you may or may not know about."
When I find stuff, (and I always find stuff), I always point it out and state; we'll do our best, or that's pretty deep.. that may not come out, etc.. The point is, I make mention of it... so it shows I see it, and I make them aware I see it and note that there may be not much I can do about it. What's cool is when I can, so it's one of those low expectations, high on execution.
I had someone ask me about the leather seat bolster cracking. One thing I always say is, we can clean it, but we can't put material back that isn't there any more. I always say, I can refer you to an upholsterer and they say "ah, no it's ok..."
Thus, it's really all in the VIF and going over the VIF w/ quote. Sadly even if you did, sounds like it was the wife (who wasn't originally present) that got upset. That's a tough one to get around when the person your dealing doesn't relay that info, or it isn't even their vehicle!
Now here is an interesting one. My wife, formerly known as Interior Gal (who quit on me last fall... subsequently leading to my fade-out/burn-out, or whatever you'll call it) is in advertising arts (as well as being a nationally certified/state-certified massage therapist and Well Coach), going back to the days pre-Mac's and Adobe, thus some stuff had to be made by hand. She's great with xacto knives! (not when doing massage tho…)
We detailed a cool old Dodge Ram that had a plow switch mounted on the dash. There was a little piece of acetone that went around the switch to protect the aluminum front. Sadly it was all dry and cracked. She went to her flat-file, grabbed some new acetone, her xacto-knife and quickly did the repair. The owner was blown away by that little fix. She did one other one for the same customer on one of their Merc's but can't remember. Again, quick on her toes and great with manufacturing.
In other words, do what you can... do the VIF, take pics, point stuff out, set expectations, be reasonable... but remember, we can't put back what isn't there (with a caveat...).
Not much for you to do now... except move on.