I've tried creating a group in oxide and check that there's no permission currently tied to that group yet the player still able to benefit from the mods that is installed in a server.

Anyway I could remove all plugins permission to a group so that said group will experience the server as 100% vanilla?

At the moment, you'd have to remove the group and re-create it without granting the permissions that you may have granted to it. There's no native command to remove all permissions from a group at the moment. Groups will only ever have the permissions that you grant to them.