By default, all Factorio servers install the Space Age DLC, as a mod. To disable this if you want to only play with the base game:
Stop your server from the console tab
Open up mods/mod-list.json
Change elevated-rails, quality and space-age to false
Go into data
Delete elevated-rails, quality and space-age directories.
Start your server
To update your Factorio server, simply run the Reinstall from the Settings tab in the control panel, don't worry, your saves are safe!
Space Age DLC will be automatically installed with the latest update.