It can vary depending on the circumstance, but often times the airlines will do this when the original flight was diverted, cancelled, or delayed for one reason or another. As an example, in the past, we've seen flights that took off as usual, but had to return for a mechanical problem. Once the problem was repaired, they took off again with the same flight ID, but a "D" was added to the end of it (I can only assume for "Delayed" or something).
Hope this helps!