Christ, dude, they're asking for a disclaimer in the description. There are true problems with the App Store review process, but this doesn't strike me as one. Add the line and get your app in the store.
The people reviewing submitted apps are just that: people. They sometimes make mistakes just like you and me. If you're unlucky an overzealous reviewer looked at your app, or someone misinterpreted the guidelines. Could be anything. Or maybe Apple simply changed their guidelines and you have to comply, as an end-user I can see why Apple would want to include a warning about battery life for apps that do continuous GPS tracking. Big deal...