What steps will reproduce the problem?
1.  Starting address 325 Berry St.
2.  Ending address Fisherman's Wharf
3.  Most bike friendly route preference

It routes you west on Berry St. to 7th St., but Berry is blocked where it
crosses the Caltrain tracks.  You have to go around Caltrain on 3rd or 4th
St. to Townsend, and take Townsend to 7th St.

The rest of the route is fine, but I'm surprised it did not pick east on
Berry St. to 3rd St, 3rd to King, King-Embarcadero to Fisherman's Wharf.

Using http://amarpai.com/bikemap/