Copying the main site to the subdomain

I had a site.com and needed to copy it on the subdomain sub.site.com.
I did it, both sites (on main domain and subdomain) works good, but I noticed an issue. Some changes on one of them affect on the other one. For example, I installed some plugins on the main domain site and after that saw a warning in the subdomain site wordpress admin panel, that the same plugins have an error because of missing files (as I said I even didn’t install them on the subdomain site). How to fix this “connection” between the sites?

Thank you!