There are some "normal" circumstances that would cause this. Aside from automatic re-routing to minimize traffic delays, the most likely is your previous direction of travel. You may have noticed that the beginning of your route(s) are sometimes obviously inefficient. This is because TomTom tries to keep you traveling in the same direction that your were traveling when you arrived at your current starting point.
For example, my house is about 600 feet from a major intersection. When TomTom is guiding me home, it takes me from that intersection, along my street, right to my house. When I then use TomTom to guide me somewhere FROM my house, the route starts out by continuing AWAY from that intersection, even if the calculated route takes me through that very same intersection less than one mile into the calculated route. However, if I didn't previously use TomTom to guide me home, it starts out with an "unknown" orientation, and calculates a route that takes me directly to that intersection.
If the differences you're seeing are at the beginning of the route, this may be what you're experiencing.