Install Drupal in a subfolder of an existing website
Drupal and Magento both use .htaccess rules for functionality.   One slight quirk with Apache is that .htaccess is processed from a directory up through all of the parents.  This means that if your Drupal install is inside your Magento install, Magento's .htaccess may interfere with Drupal (a Magento directive may be applied after a Drupal one).  This is going to totally depend on your setup.  At very least, you will likely need to set RewriteBase in the Drupal .htaccess for things to work properly.  I have seen similar situations work perfecty fine, but others fail in bizarre ways.