I think this not an Google Map Issue. This is Expected Scenario.
If in your current Selected Route any tolls are there then only it will show those options, In your current routes ferries are there. So, you are getting that in your route options.
I believe that this is because you have the cycling option chosen. When I start a bike route, I only have the option to avoid ferries. When I switch it back to a driving route, the options that you are expecting to see return for me.