Sorry
@Collin Kaufman. As an instructor in the past (not CFI) I put most of the blame on the training. I went through at least 6 instructors for my instrument ticket because I had that luxury (not everyone does) and I wanted to get different perspectives. Any CFI's familiar with the law of primacy? Remember that its easy to say "know your stuff", but if the student is relying on you to be the expert and you are training them wrong, it's harder to then retrain against those habits. Especially not during a checkride, sheesh. I would probably not actually trust the instructor in the future to be completely honest.
Yes there is responsibility on the student's end to be fluent in the FAR's for safe IFR flight, but what if you knew you were right and someone in a position of authority was telling you that you were not? Would make you second guess yourself, no? Perhaps that instructor was even training you a little haphazardly because either they didn't understand the rules or didn't care enough to teach them properly, how would you know if you constantly got the "atta-boy"?. You learn to accept that is "OK".
@Collin Kaufman even said he flew that 20 times the wrong way because the instructor said that was the way to do it.
Bad training is bad training. Sounds like this was just the perfect storm of training and timing gone wrong. You'll get it though, just remember not to put your instructors up on some pedestal because they have some fancy credentials. They are there for you and without you, they don't really mean much. And..always question when you think something is wrong. The really bad instructors (the ones you should run from) will have a problem with this, get angry, or defensive. The really good ones will be able to explain and reference exactly why you are doing what you are doing in a way that makes sense to you.
Good luck on your next ride!