NOTE: this answer only refers to older devices, around 2015 and before.
You are not doing anything wrong. If you create a route, you should be aware that in fact you are NOT pointing out a route, but ONLY one or more waypoints. You feed these waypoints to your TomTom device and it will calculate a route, using the waypoints that you gave it and using the conditions that you have entered (avoid highways, fastest route, shortest route, etc.).
Therefore, it is always important to place your waypoints properly, to make sure your TomTom device will lead you the way you want: the locations you want to be or the locations you want to avoid.
This also means the following: you cannot trust the route lines in Google Maps blindly. Your TomTom device may calculate another route (using the conditions you have entered) than Google Maps. That is why it is important to use enough waypoints: the more waypoints, the more accurate the route will be. (A waypoint on each step of your route would guarantee a super accurate route, but that is impossible to do, of course.)
You should also realize that the map in your TomTom may be different from the map that Tyre is using (from Google). One of them may be more actual than the other one. Or there may be errors on one of them.