If the App Store detects that your Mac can install a newer OS than El Capitan it will refuse to download El Capitan.
What Mac, model and year are you trying to download it for. You say you have one of your MacBooks already running El Capitan, open the App Store Purchased page and see if you can download it that way. If it downloads then once it has completed look in your Application folder for Install OS X El Capitan.app, if you find it copy it and move it to your other MacBook and install it that way. In fact try signing in to the App Store using the Apple ID you use on the MacBook that has El Capitan installed, go to the Purchased page and download El Capitan that way. Make a copy of the install app in your Applications folder before starting the installation and keep it somewhere safe, the one in the Applications folder self deletes on completion of the installation.