Then you don't want to be in the electrical business do you? The OP isn't a contractor but instead an inspector, so the credit issue doesn't apply to him, but having been involved in many, many projects that have been value engineered and/or have specs that aren't compatible with each other, I can think of a dozen valid arguments right off the top of my head on how I would fight a request for a credit for plastic boxes. It very much depends on the situation. There is just no valid reason to require metal boxes with NM cable. If you are going cheap, then go cheap. Engineers are subject to the same problems the rest of us are. They have boilerplate specs, and they don't get paid enough to go through every item of a spec and make sure that it is perfect, so they miss things like this when a job is outside their normal spec wheel house. As an estimator it should be picked up an and at least clarified in the bid, but sometimes the estimator is under the same constraint.
It is extremely unlikely that I would give back a credit for this on a job I estimated and ran. I have spent years honing the skill of identifying counter arguments. One of the best ones is that you always pay attention to the little things you do because you know they must be done even though the plans don't indicate it properly. Like when they show hash marks on a plan and the number of wires is wrong. You don't pull the wrong number of wires, you just do it. That becomes very handy when you explain that you didn't install (or price) metal boxes when plastic was in line with the intent of the drawings, you just did it.
The OP just states hes an inspector. If he is an inspector or owners rep he has every right to ask for a credit. If I was doing the 3rd party inspection this is what I would do.
The following is only based on what we know about this project.
Ask the contractor why he used plastic boxes when metal boxes were specified. I would require the answer to be in writing. I would then inform the owner as to the situation and the options available to him.
There are 3 options here.
1) Keep the plastic boxes and do nothing.
2) Keep the plastic boxes and ask for a credit.
3) Change all the plastic boxes back to Metal.
My recommendation would be keep the plastic boxes and take a credit. I know you said you can defend not issuing a credit. I would just reply then we want the steel boxes, its in the specs.
I hope you are not the guy that we just did an inspection on where he has all aluminum busing on his switch gear and panel-boards when copper was specified. This goes for all the feeders also where he changed them from copper to aluminum. Hes in a world of crap. He submitted all copper even on the switch-gear. After everything was approved someone (EC we think) changed the package to AL to save himself a good chunk of money. All I do is file a report. I am pretty sure this one is going to court. I will give him credit he did re-size the feeders.
Does it work? yes
Does it meet code? yes
Does it meet what was specified? No