I used an external addon in my app then i decided to delete it but the plugin that provided by this addon is still in the project.
This should not happen. Perhaps you didn't remove the addon completely - right-click your project name and check "View used addons" under Tools.
Another possibility is that the same Cordova plugin is required by some other addon or even by an official C3 plugin. In this case removing it with CLI may break the game.