Another reason not to use Romex... anytime you attempt to nail up wire that's not much different than zip cord, it can happen. Almost impossible for it to happen with BX or MC -- unless you're pounding on it like it's a ground rod, or trying to demo the studs down.
I'm surprised the inspector even picked it up -- obviously she had WAY too much time on her hands. Most inspectors around here would've never caught it, since I doubt it was as bad as you say -- otherwise you would've caught it. It didn't nick the insulation, did it?
Don't feel bad about some government bureaucrat red tagging your work. Many have never held a linemans pair of pliers in their hands, or stripped a cable. For some inspectors, it's their life's work to be a big pr_ck, and their day wouldn't be complete if they didn't tag at least one job -- no matter how neat, workmanlike, and code compliant it might be.
And NO this is not to take a swipe at ALL inspectors, many are from the trade, know their craft, and are a pleasure to deal with.
Joe