Sorry about being brief, but a lot of this is covered in the wiki www.waze.com/wiki

Unless the lock segment is checked on a one way segment, waze may attempt to use them when no given a better option. This is due to the fact that waze cannot for sure know about all the two ways until someone drives them are sets them correctly in cartouche.

To fix this, you will want to make sure the geometry of all the segments is correct.
Then set the directionality correctly, and also checkmark the lock option in the edit details.
Then for the junction that connects them, highlight it and restrict all turn, enable all turns, then put in any real restriction that aren't covered by directionality restrictions.

It sounds long, but it really isn't in practice. And is just part of my normal routine when working a problem.

And to quickly expand, if an overpass is involved, you will want to totally remove the junction at the overpass. You can use the "bridge" functionality of Cartouche or manually remove the junction (names and directions of roads must agree for either method to work well).

Once unneeded junctions are done, you also want to edit the level of the segments (Level in Edit Details within Catouche) to define which roads/ramps are physically above the others.

By default Waze thinks the world is flat because the basemaps started from one-dimensional paper maps.