Why is my phone failing to install an application saying its rooted?

Maybe that you have rooted your phone before?

If you haven't done anything then no it's not rooted. You can download Root Checker from the Play Store.

Some apps don't like custom ROMs so that might be triggering that warning message.

Some users reported that SuperUser Root manager is installed within. You can just uninstall it and yor're good to go.

Hope my answe will help you.