Eep! Sounds messy! Hope it works out for you.
There are two different certificates you can get from a course...one is a piece of paper that says "yes this person has attended a course in x today" and the other piece of paper would be a qualification that shows you have been assessed and are now nationally recognised as a qualified person in the subject concerned.
It sounds like the certificate you have was a "this person has attended the course" type of certificate and to get the qualification you perhaps needed to do further assessments to qualify for a city and guilds qualification.
Don't worry...the important thing is that you have your skill...if you do then you can always get in touch with another training provider who can assess you to be able to get you qualified (for example, for an nvq in nail services, you could get in touch with the carlton institute for this sort of thing)
Hope this helps