Jan,
While I have never missed a ship I have come close. I booked my own guide in Costa Rica. There was a major accident and the only road to the port was blocked for an extended period of time and I had even allowed an extra three hours of time. We literally made it to the pier at departure time. Also, one difficulty I have found is sometimes an independent will promise you an English speaking guide (as they did in Costa Rica) and all they can say is hello, goodbye, and thank you. I prefer to stick with ship tours where I know they speak English or with an independent tour guide that someone else has offered a positive recommendation. In my opinon, excursions in countries such as Brazil to outreaching areas are best with an established company.