Waze's mapping model is slightly different from all the other players in the game. Instead of buying the maps (for a hefty price) from the two companies that sell this data. They have taken government data and are augmenting it with data collected from crowd sourcing.
Routing is based off average speeds and directionality of travel based off driving habits of all waze users (plus realtime traffic data from wazers). What you are experiencing is lack of complete data for the route you think is optimal. It takes about 24-48 hours for the Waze servers to analyze our driving tracks and try to match that up to the roads it currently knows about. And that's in a perfect world, where your phone's GPS is perfect, and the map data is also perfect. If our tracks don't match up well... it might take more passes for the gaps to be filled in.
To see how well your Waze is matching up your route, check "My Dashboard" and click on the individual trips in "Your recent routes" (if you don't see any route, then the servers aren't done analyzing them yet). This will launch cartouche (the map editor) and show you your route in hopefully a green line. If you find red, then Waze was not able to match up your tracks to a road. If you are missing segments, then you might have had a network drop out and the tracks were not able to be uploaded to the server. The more green there is, the faster Waze will learn the roads on your route, and potentially use them during routing.
If your GPS is spot on, and you are seeing red, then some of the map might need to be updated to make things match up. That's where one of the benefits of Waze comes in, where we as users can update the maps to make them more accurate.
As far as map edits go, it might take a while for them to actually get down to the phone. The goal there is also 24-48 hours, but due to high popularity, I've been seeing a little longer.
I hope this gives some insight into the workings of waze, and you stay with it long enough to see the end benefits.