Do you mean Streets & Trips is re-routing to a "missed" waypoint? If this is the case, the simplest thing, when planning your route, is to zoom in very close when placing your pushpins. It is very easy to accidentally put them in the wrong lane of an interstate highway or off "route" if zoomed out too far.
Another example of misplaced waypoints is, let's say I am going to Yellowstone Nat'l Park and I want to go via West Yellowstone, MT. If I tell the Route Planner to add West Yellowstone as a via, it will place a marker right smack dab in the middle of West Yellowstone. Not exactly what I want as it will be off-route if I'm just driving through to the West Entrance of the park!
This can also happen when you leave your route for some reason (like spending the night) and return at a different point and you've by-passed a waypoint.
If you use the Hotkeys for S&T, you can pres DEL and S&T will delete the last waypoints that are behind you. Download this cool little free add-on at
http://www.laptopgpsworld.com/free-add-ons
I hope this is what you meant!