If the instructor just told you to grab your partner "as if you were in a street situation" rather than giving you the specific attack the counter was meant to work against, that indicates a problem in his teaching skills, his understanding of the technique, or both.
You might hope that your black belt training partner would have enough experience to recognize that you weren't feeding him the right attack for the defense in question and switch to a more appropriate technique. However black belt is not a very advanced rank in the Bujinkan. I don't know how it is in the BBD. Either way, he should have called the instructor over to ask for help and the instructor should have been able to correct his technique (if you were feeding the correct attack) or else correct your attack to the appropriate one for that defense and also show the correct defense to the attack you were using. When I teach that technique, I show the 2-3 most common methods for an untrained standing choke and the appropriate defense against each. If I have time, I may also show a more technical approach to applying the standing choke which shuts down those defenses.
This is all based on the supposition that you weren't intentionally just trying to mess him up and keep him from practicing the technique. If you have reasonable skills and are bigger and stronger than your training partner and are put in a highly advantageous position and know in advance exactly what technique your partner is going to try applying to you, then you should be able to shut it down and prevent him from executing that particular move no matter what the technique is, unless he is a lot better than you. You may be setting yourself up for some different technique, but you should be able to stop the specific move which was indicated beforehand. Generally the only way you get to tell someone ahead of time exactly what you are going to do and execute that exact move despite their best efforts to stop you are if you are much more skilled than them, have much greater physical attributes, or get to start out in a much superior position.
I'll assume you weren't trying to be a bad training partner in that sense and turn it into a sparring session where you got to start with a dominant position. If you were just trying to follow the teachers instructions and grab your partner's neck the way you were told and your partner wasn't able to make the technique work and the instructor didn't come by to fix the situation, then that would seem to indicate a lower level of instruction than you should be looking for.
