As far as I remember, annotating embedded fields with @Indexed will not work. @CompoundIndex is the way to go:
@Document(collection = "user")
@TypeAlias("user")
@CompoundIndexes({
@CompoundIndex(name = "contact_email", def = "{ 'contact.mail': 1 }", unique = true)
})
public class User {
@Id
private ObjectId id;
private Contact info = new Contact();
}