Because no one is perfect, no server is perfect, and trough time changes are necessary.
Speaking of flaws in server, even hundreds of millions of dollars companies such as Blizzard make changes and has bugs to fix regularly.
Same applies for Gravity, eAthena, and each individual private servers.
If you speaking of dramas, and people complaining about imbalance issues, the only reason why official servers doesn't have as much complaints or dramas is only because they don't listen, and people have to "Live with it" which eventually they get use to it and forced to accept it. They can't go to GM's saying "This is imbalance LOL WHAT U THINKING" nor complain in ratemyserver.