namespace Project2.Model
{
    using System;
    using Xtensive.Orm;

    [Serializable]
    [HierarchyRoot]
    public class BaseClass : Entity
    {
        public BaseClass(Session session) : base(session)
        {
        }

        [Field, Key]
        public int Id { get; set; }
    }

    class Children : BaseClass
    {
        public Children(Session session) : base(session)
        {
        }

        [Field]
        public bool SomeBool { get; set; }
    }
}

program.cs

    using System;
    using Xtensive.Orm;
    using Xtensive.Orm.Configuration;
    using Project2.Model;

    namespace Project2
    {
        using System.Linq;

        class Program
        {
            static void Main(string[] args)
            {
                // Loading configuration section for in-memory database. 
                // See other cases in App.config file.
                var config = DomainConfiguration.Load("Default");
                var domain = Domain.Build(config);

                using (var session = domain.OpenSession())
                {
                    using (var transactionScope = session.OpenTransaction())
                    {
                        var t = session.Query.All<BaseClass>().ToArray();
//Work ok
                        var k = session.Query.All<Children>().Where(a => t.Contains(a as BaseClass)).ToArray();
//But without cast we have fail
                        var m = session.Query.All<Children>().Where(a => t.Contains(a)).ToArray();

                    }
                }
                Console.ReadKey();
            }
        }
    }

It's ok or bug?