So, I am the owner of a server. When I go on my server and find a hacker or greifer, I use /ban [USERNAME HERE]. Instead of banning that user, I get a message saying - in red - CubedCraft > you have no perms!
I am the owner with the owner tag, but I can't do anything (I am oped too)! I will put the image of this as an attachment to this. Thanks!

~Peri/Trash_Heap 

The ban/tempban/kick/mute/unban commands are from our bungeecord since we staff have a global system

So u need to use e like /eban 
There is a new way under development but will take some time before its ready