With some apps (e.g. early bittorrent clients) the 99.9% problem happens because of this:

1. Your client requests the final piece of a file from somebody.
2. This somebody either logs off after this, or queues you way down in his download queue, or chokes you (on bittorrent) or just has a veeeery slow upload speed.
3. Your client is stuck with downloading from the other client at a very low speed (Or is waiting in queue, or is retrying a dozen times before it gives up), and you are stuck with 99.9%.

Newer p2p clients often fix this problem by using something called "Endgame mode": When only one piece is left, this piece is requested from all other peers at once.