Upvote:5
There may indeed have been people there who were not known to be there by anyone, think possible homeless people squatting in the parking garages, and visitors from out of town with no relatives or friends to report them missing (or everyone who could report them were themselves there and died).
The second category is probably small, given the early hours of the attack and thus not all of the businesses in the buildings were already open (The offices of the company I worked for at the time were for example empty, as they wouldn't start work for another hour or so, the staff were on their way to work when the aircraft hit and all survived).
Most of those people who died will have been found and be part of the unidentified dead, but some bodies will never be recovered because there just wasn't enough left to identify as human remains.
And some of the unidentified will never be identified as there is for example no DNA of them on file anywhere, no dental records (if enough of the jaw survived to yield those).
This is generally the case with all large events that don't affect a narrowly defined group of people (like an aircraft accident, there are lists of everyone on board of those for most all flights).