WARNING: This page is about a different car, the 2014 Volkswagen Beetle, 2013 Volkswagen Beetle, and 2012 Volkswagen Beetle. However, it is still accessible from the selected car via links, so may be relevant.
To prevent foreign objects from entering when working on the engine, seal open intake and exhaust channels with suitable plugs, for example from the Engine Bung Set VAS 6122.