Is it possible for an applicant to be disadvantaged by negative comments sent via emails without his/her consent? I saw some reports about how corrupt teaching staff in some colleges in some countries forces their students to comply with their unreasonable demands (e.g. to conceal a huge flaw in the teacher's research, or to stop speaking their own native language) by threatening to write negative emails and letters to disadvantaged their students' job or academic application. 

Of course, such teaching staff will, hopefully, eventually get punished. (Note that we cannot always find evidence of their unethical behaviour, so some get away with it.) But even if they are punished, there is probably no means to stop them from making negative comments directly to the admission office or even one or two professors/employers who make the final decision.

What should students do to protect their own rights? Is it likely that some real damage will be caused by such malicious emails?

Some may complain that I should not ask this because it is not happening on myself - but the situation I describe is NOT hypothetical, and it might happen on anyone, so it is helpful to know how to tackle the situation.
This is a supper difficult problem and is responsible for much of what is wrong with academia. 

Its definitely not unheard of for a recruiting academic to call contacts at institutions a candidate has been associated with and ask. 

If you are in Europe, and you are turned down for a job you were sure you were the best candidate for, you can issue a GDPR demand to the universities in question, and they must turn over any materials that contain information about you. This should include both formal and informal references. Obviously if the bad-mouthing happened over the phone, there will be no record of it, which is exactly why people often use the phone for this sort of thing. 

You could then try claiming that the university treated you unfairly in the hiring process. You'd have to be careful because the university could try saying "We didn't select this candidate for other reasons, nothing to do with the reference. Here is the documentation that lists the criteria we used and the candidate's scores". 

You could also try suing the phantom referee for libel/defamation if you were really into long drawn out legal battles.