It's almost impossible for us to tell without seeing application AND removal of your enhancements as to where the damage occurred. Note that it's only the application / removal that has the potential to damage, not the product itself, so whether you had gel or acrylic doesn't make a difference.
However what you said about having an electric file on your natural nail is definitely not right and I'm almost certain that this where the damage would have occurred in your case. Unfortunately if your nails are thinned due to this, the only remedy now is to let the damage grow out.
In the future, the things to look for in a reputable, safe nail tech are (as well as not using electric file on your natural nail lol):
The place should be clean, all instruments disinfected
Tech happy to show you their qualifications and public liability insurance certificates
Acrylic or gel products should be in manufacturers containers (or you should at least see these being transferred from the manufacturers container to the dishes-this will be an indicator as to whether the product they are using is designed for nails-as many use products that are not, which require roughing up of the natural nail unfortunately).
You should be given proper aftercare instructions including the use of cuticle oil daily and proper maintenance and removal instructions.
Removal should not require filing of the natural nail or pulling off the enhancements.
Nothing should be painful!
Hope this helps xx