When defining order-by in collection mappings, NHibernate does not qualify order-by with table name if Sql Server is used. It does work with Sql Server CE, though.

gistfile1.cs

// uncomment this to use SQL Server instead
#define  USE_SQL_SERVER_CE

namespace AmbiguousColumn
{
    using System;
    using System.Collections.Generic;
    using System.Data.SqlClient;
    using System.Data.SqlServerCe;
    using System.IO;
    using NHibernate.Cfg;
    using NHibernate.Cfg.MappingSchema;
    using NHibernate.Connection;
    using NHibernate.Dialect;
    using NHibernate.Driver;
    using NHibernate.Mapping.ByCode;
    using NHibernate.Tool.hbm2ddl;

    public class Node
    {
        public Node()
        {
            Children = new List<Node>();
        }

        public virtual int Id { get; set; }

        public virtual IList<Node> Children { get; protected set; }

        public virtual Node Parent { get; protected set; }

        public virtual int Position
        {
            get { return Parent == null ? -1 : Parent.Children.IndexOf(this); }
            protected set { }
        }

        public virtual void AddChild(Node child)
        {
            child.Parent = this;
            Children.Add(child);
        }
    }

    public class Program
    {
        public static void Main()
        {
            var compiledMappings = MapModel();
            var config = ConfigureNHibernate(compiledMappings);

            using (var sf = config.BuildSessionFactory())
            using (var session = sf.OpenSession())
            using (var txn = session.BeginTransaction())
            {
                var children = session.QueryOver<Node>()
                                      .Fetch(x => x.Children).Eager
                                      .List();

                txn.Commit();
            }
        }

        private static Configuration ConfigureNHibernate(HbmMapping compiledMappings)
        {
            var config = new Configuration();
            
#if USE_SQL_SERVER_CE
            ConfigureSqlServerCE(config);
#else
            ConfigureSqlServerExpress(config);
#endif

            config.AddMapping(compiledMappings);
            new SchemaExport(config).Execute(true, true, false);

            return config;
        }

        private static HbmMapping MapModel()
        {
            var modelMapper = new ModelMapper();
            modelMapper.Class<Node>(cls =>
            {
                cls.Id(x => x.Id, map => map.Generator(Generators.Identity));
                cls.ManyToOne(x => x.Parent, map => map.NotNullable(false));
                cls.Property(x => x.Position);
                cls.Bag(x => x.Children, 
                        map =>
                        {
                            map.Inverse(true);
                            map.Cascade(Cascade.All);
                            map.Key(key => key.Column("Parent"));
                            map.OrderBy(child => child.Position);
                        }, 
                        map => map.OneToMany());
            });
            var compiledMappings = modelMapper.CompileMappingForAllExplicitlyAddedEntities();
            Console.WriteLine(compiledMappings.AsString());
            return compiledMappings;
        }

        private static void ConfigureSqlServerExpress(Configuration config)
        {
            config.DataBaseIntegration(db =>
            {
                db.Dialect<MsSql2012Dialect>();
                db.Driver<Sql2008ClientDriver>();
                db.LogFormattedSql = true;
                db.LogSqlInConsole = true;
                db.ConnectionProvider<DriverConnectionProvider>();
                db.ConnectionString = new SqlConnectionStringBuilder
                                      {
                                          DataSource = @".\SQLEXPRESS", 
                                          InitialCatalog = "AmbiguousColumn", 
                                          IntegratedSecurity = true
                                      }.ConnectionString;
            });
        }

        private static void ConfigureSqlServerCE(Configuration config)
        {
            if (File.Exists("data.db"))
            {
                File.Delete("data.db");
            }

            File.Create("data.db").Dispose();

            config.DataBaseIntegration(db =>
            {
                db.Dialect<MsSqlCe40Dialect>();
                db.Driver<SqlServerCeDriver>();
                db.LogFormattedSql = true;
                db.LogSqlInConsole = true;
                db.ConnectionProvider<DriverConnectionProvider>();
                db.ConnectionString = new SqlCeConnectionStringBuilder { DataSource = "data.db" }.ConnectionString;
            });
        }
    }
}