You appointed Lydia steward, unless she is dead, she is still steward for that house. So you have several choices, kill her and appoint another steward, leave her as your steward, or load a save game before you made her steward and go find someone else. Having your steward as a follower does not mean you can have two stewards for the same house.
If you stuffed around on the PC with console commands you are going to have to use a console command to fix it.