If you use HTTrack with its defaults, then you are leaving clear indicator
already by the browser id. So yes.

If you change the browser id to simulate for example an Internet Explorer
coming from a Windows 10 machine, then you still leave a trace, but as an
IE+Win10 machine.
However, smart web log analysers can certainly tell the difference (or at
least with high probability) if their website got crawled by a mechanism or if
that was human interaction. 

And any interaction with any website will leave traces of your IP address
always. This is of course no different with HTTrack.