Autofac does its session disposal through an HttpModule called Autofac.Integration.Web.ContainerDisposalModule.

You need to either

• Put your own session cleanup in a module that is run before the container disposal. This can be a problem as the order of HttpModules is not guaranteed.

OR

• Remove the Container disposal HttpModule from the web.config and do your own lifetime scope cleanup in your Application EndRequest

private void Application_EndRequest(object sender,EventArgs e)
{
    ISession session = ContainerProvider.RequestLifetime.Resolve();
    //cleanup transaction etc...
    ContainerProvider.EndRequestLifetime();     
}

OR

• Create a session manager class that is IDisposable and lifetime scoped,take your ISession as a constructor dependency and do your session cleanup when it is Disposed at the end of the lifetime.

public class SessionManager : IDisposable
    {
        private readonly ISession _session;
        private ITransaction _transaction;

        public SessionManager(ISession session)
        {
            _session = session;
        }

        public void BeginRequest()
        {
            _transaction = _session.BeginTransaction();
        }

        #region Implementation of IDisposable

        /// 
        /// Dispose will be called automatically by autofac when the lifetime ends
        /// 
        public void Dispose()
        {
            //commit rollback,whatever
            _transaction.Commit();
        }

        #endregion
    }

You must make sure to initialize your session manager.

protected void Application_BeginRequest(object sender,EventArgs e)
    {
        SessionManager manager = _containerProvider.RequestLifetime.Resolve();
        manager.BeginRequest();
    }