If you see such message from the tracker (to many downloads, or as well time outs), what you can do to have your upload and download tracked is the following:
Do not stop that torrent and keep the torrent programme (e.g. µTorrent) running. If you stop it's over.
Stop other downloading torrents from the same tracker, that will free slots to connect to the tracker
Try to update the tracker for the red torrent after having stopped other 'green' downloaing. There is a minimum time between tracker updates, the function is greyed out if an update was attempted recently, you may need to wait a few minutes. In µTorrent it is on the drop down list on that torrent in the torrent list, the before last item of the drop down list.