Is it a violation to influence the training/certification of a unit conducting an MRE? What AR is violated and how do I report it?

Having been in the OC/T world....OC/T really just validate what the Commander wants to train on.

Commander: I want to train on (insert METS)
OC/T: Ok. I'll evaluate you on your TE&O based on that METS.

If there is conflict with this scenario...you do not try to solve it. You inform your CHOT and let them engage.

For every evaluated exercise, the unit CDR is in charge. Period. Even at the NTC. It takes OC/Ts a while to understand that. Very few, if any, exercises "certify" a unit for anything. A unit shows up, conducts their METL tasks, gets a report card, and leaves. The report card is used by their higher command to assess the command team and the unit for effectiveness. External evaluators, even if they are generating mission orders are in no way in charge of the actual training.

While the unit in charge of conducting the facilitation of training and evaluation has a plan for what tasks they will look at and what injects they are executing to prompt those tasks, CDRs of training units have a lot of leeway to conduct the training they deem appropriate based on their METL priorities or DMETL assigned by higher and have every right to request an evaluation of those tasks. Traditionally, and more efficiently, these "wants" are discussed with the facilitating unit during the IPR process. But so many things get overlooked. Most facilitating units try to stay very flexible to get their job done and accommodate what unit CDRs want to get done.

It seems you have two separate issues:
1. if the CDR is being disrespectful, pass that up your chain of command during your AARs with them. Very few interactions with a unit commander by OC/Ts end well if the OC/Ts stop being professional evaluators. Remember, they don't work for the evaluators nor the facilitating unit command. Stay professional, try to bring concerns to your OIC and let them deal with it.
2. if the issue is that the CDR is requesting training or evaluations of training that the facilitating unit or the OC/Ts were not prepared for or expecting, such is life. A good CDR will want to assess as much as they can, especially if they are preparing for a mobilization or taking on tasks they have not had a chance to have evaluated in the past few years.

Just remember, there also may be some unprofessional actors out there that is coloring the CDR's interactions with the OIC. Example:

My unit was at the NTC with 3ACR and about halfway through, we finished up our mission and rolled into the BN battle position. The BN had 50% security, so we pulled our own BP inside of theirs and established 75% security on an outer ring, pulling the rest of the tracks inside the circle. The gunners of the inner vehicles stayed in their turrents. A few of them had M249s sitting next to the M2 (just in case), but not mounted. They were instructed to sleep in the hatch. In the early morning a OC/T walked past both lines, to one of the inner vehicles and grabbed the M249 saying it was "unsecured" and took it to his OIC. What followed was a former marine (now Army CPT) verbally stomping a sloshy mudhole into the whole group of them. Maybe unprofessional, but the OC/Ts wanted to play silly games that made no sense given the circumstances. Sure the BN CDR gave him a talking to, but he understood the situation.

Short answer: Report observed improper behavior through your chain of command (however, you better read though to the end).

Long answer: I gather what you're describing is not so much as something that is "illegal" or "against the rules" (unless you installation/organization has policies regarding unit interaction) but rather something that is unethical in your view. This is the nebulous world of AR 600-20 and FM 6-22.

In other words, your saying that you don't believe the Commanding Officer of the unit is living up to the Army Values they are supposed to embody. If their conduct was so egregious, I assume you wouldn't be on RallyPoint looking for suggestions on what to do.

To your specific incident - A Command Officer trying to influence OC/Ts is something that occurs frequently. Should it? No, but it does. This is one of the reasons that the senior OC/T will ideally be at least equal in rank to the unit they assess.

However, I'm not sure this is your fight. The role of an OC/T embodies a situation you'll encounter numerous times - a conflict between what you should do and what others want you to do. Most senior controllers or OC/T OICs will be told by senior leadership the DOs and DON'Ts regarding their job - and one of the big ones is to be firm about what is required of them and that unit leadership will often try to dissuade them from that. However, they work for the MTC commander, not the unit commander being assessed.

Have you talked with the OIC that was trying to be influenced? If not, why not? It's possible they have already handled it at their level and it's a non-issue (I.e., "Sir, I'll remind you that I'm required to assess A, B, and C. If you don't allow me to do that, I'll have to fail your unit and discuss why with the MTC Commander.")

If you have, and depending on which unit you are in, there's a possibility that a Senior Mentor (usually a retired senior officer) is assigned to coach that commander of the unit. If one exists, I suggest you have a discussion with them.