example.com and example.com/this

Here is how the data accrues if
Site 1 is littlefurnace.com/info and
Site 2 is littlefurnace.com

You can see the overlap, marked in yellow and blue, below.
But there will be no overlap if I use the default code. To return to that default code, I just need to remove four lines that I forgot I had put into my Matomo JS tracker script in the header of my website.  Main point: A URL with a subdomain, or a subpath can visually look like it will tell littlefurnace.com AND littlefurnace.com/info bout my visit, but it can't unless my ten lines of JS in the HTML header have both of my websites listed.  If you scroll down to my code, you see I have a line that reports Site ID = 1 and Site ID = 5. If I remove the lines about Site ID  = 1, there will be no tracking data sent to Site 1 (littlefurnace.com). 

In other words, you can prevent the domain from tracking the subdomain by simply altering the script you insert in the header of that served site page.

What about the opposite: you DO want the data to go to two site IDs? You can adapt from my code below. The official guide is here:
 matomo.org/faq/how-to/how-do-i-send-tracking-requests-to-two-or-more-matomo-servers/