Though this post is a bit old, what you can do to sort of get around this is
the following:

once your original project is done, open up the error log that wintrack will
show you. If they are pages it missed for whatever reason, these are usually
at the top of the error log file.

copy/paste these into your own notepad file and save it. Now take a look at
the errors and fix why they did not download. Example, in my case I had some
html files that were like this: somelink.com/html) it listed a parenthesis at
the end of the link. Removing that and just using the link - 
somelink.com/html  the page I needed showed up in my online browser just
fine.

So go through them and once you fix or do what you need to do, start a new
project in winttrack and enter the correct urls you needed- now download them

Once done, in your original project that listed them as errors, go the page of
where it should be linked to. Example website A on page 1 if I click the first
link would normally bring me to a page that wintrack gave me an error on.

using an html editor or even word/note pad- edit the html page and change the
link location to where the corrected and newly downloaded file is. So using my
top example Website A was the original site. Website B is my second project
used for the pages it gave errors on. I now edit the link on Website A to
point to the correct file in Website B (or where-ever you choose to put it). 

This dirty workaround will fix your problem

basically you are just checking/fixing whatever pages wintrack gave you errors
on. RE-downloading the error pages after fixing them and then changing the
links from your original download to point to the new link locations of the
working files