So it seems on file backend PermissionsEx works completely fine but when you import a backend file into a database and then try to load PermissionsEx and it tries to load the permissions just recently uploaded it returns a MySQL error saying that the option "prefix" is not found.

Correct me if I'm wrong but either the "prefix" option for ranks is not being added in proper through the pex import file command or the prefix option is stored somewhere else in MySQL?

Unfortunately PermissionsEx is currently unmaintained and no further updates are planned. Because of this, all issues are being closed. If you are looking for an actively maintained permissions plugin, take a look at LuckPerms. It is compatible with major server platforms and can import data from PEX.