There is nothing wrong with writing a letter to the CAA's licensing/safety group which describes what you have seen whilst making it clear that this was at a time of limited experience and (if you are like most students) substantial stress.
Written in a manner that you would be prepared to stand by around a table with a CAA rep and the CFI, there's no reason to keep this a secret.
Sad to say, I have been in exactly your position as a student at a helicopter training organisation, which is why the comments may have rung a bell!
I trained at a small school for 30 hours then left, joining another school about 6 months later. I immediately realised that there were many issues at my old school. I discussed them with the new instructors and the CFI at the new school, then called the CAA. I could have called the old school but unfortunately the instructors who had taught me had also left the school and I had moved away and did not want to do this over the phone.
I discussed the matter with a member of the CAA safety group, frequently mentioning that it was easy for me as a student to get the wrong impressions. They told me to write it all down, and that what they do is to keep all these issues in mind when arranging inspections - it gives them information about what to look for. Such letters are not that unusual.
I was not contacted again, but if I had been I would have had no problem discussing the letter at a meeting because it just stated what I thought I had seen and did not judge the school. If the CFI had disagreed, he was obviously welcome to his opinion and the CAA can make their own judgements taking into account our relevant experience.
We are all collectively responsible for each other's safety in the sky, and badly trained pilots will hurt everyone, so just as when in a light aircraft I would not hesitate to tell a pilot that I was uncomfortable with the current flight situation (one dissenting voice), you should voice your discomfort.
Would you tell an experienced pilot if you were uncomfortable with a flight situation and ask him to explain how it was safe or make changes to it? I hope so, and hope even more that he would listen!
Don't think of it as being a troublemaker, think of it as acting responsibly by letting those who are qualified to regulate schools do their jobs.
BW