Note: these steps are for the special case where a user wishes to submit a Xamarin.iOS app to the App Store using the Xcode Organizer. In most cases the simpler option is instead to use Application Loader. See the first post on https://forums.xamarin.com/discussion/40388/disallowed-paths-itunesmetadata-plist-found-at-when-submitting-to-app-store/p1 for the simpler steps and additional information.
For this example assume that the name of the Xamarin.iOS project is "iPhoneApp1".
(Modified from the helpful post here.)
- 
Use the "Build -> Archive for Publishing" workflow in Xamarin Studio to create the
.xcarchive(see also the "Building the Distributable" section on the publishing guide). - 
In Finder, locate the
.xcarchiveunder~/Library/Developer/Xcode/Archives. You can paste this path into "Finder -> Go -> Go to Folder" to browse the folder. Look for the.xcarchivefolder under today's date. For example:2015-05-07/iPhoneApp1\ 5-07-15\ 4.25\ AM.xcarchive. - 
Control-click the
.xcarchiveand choose "Show Package Contents". - 
Navigate to
Products/Applications/iPhoneApp1.app. - 
Control-click the
.appbundle and choose "Show Package Contents". - 
Find the
iTunesMetadata.plistfile and move it to trash. - 
Open the
.xcarchivein Xcode's Organizer, for example by navigating back up the folder hierarchy and double-clicking it. - 
Submit the app using Xcode's app submission workflow.