This seems local. I just checked routing from North Berkeley to Emeryville and Apple Maps routes me down the main north-south traffic sewer instead of good parallel bike routes, and Apple Maps appears unaware of the new bridge across the rail yard. Google's results are far more sensible.
Exactly this. I'm sent down Sacramento or San Pablo regularly, instead of the California or King st boulevards. Most people who ride around don't need the directions, but now and then you see someone you can tell is following them, not realizing there's a far safer option around the block.