The PTM is a little more than that.
The PTM contains the directives that govern all aspects of the training process, from classroom phase to in-hull, oral boards, tests, etc.
Also, how poorly is poorly, related to your performance. If your performance was poor, with no indications that your performance would improve with continued enrollment, then they are well within the rules and regulations to disenroll you.
The Nuclear Navy is based on procedural compliance. The PTM is one of these procedures. If you are saying that the prototype staff intentionally and maliciously violated this procedure in order to disenroll you, that is a serious accusation. Keep in mind that you are still on active duty. As such you can and will be held accountable for any statements that you make in a public forum (and yes, the internet is most definitely a public forum) if these statements prove to be baseless or without justification.
I don't say these things to scare you or take the Navy's side. You need to keep these things in mind as they are YOUR responsibility as an active duty member. You need to remember that your performance is YOUR responsibility. If it was not up to par, then you would be disenrolled.
Lastly, when you discuss things here please be specific as to who "they" are. These infamous people are responsible for uncounted atrocities worldwide. On a serious note, if we know specifically who "they" are, we can tell you if you are talking to the correct people or not.