Favourite can mean the one you like the most, where as best is the one you think is of the highest quality. Both are still just opinions, but I can see how they might not always be the same.
For example, "That album is my favourite because I can still remember hearing it for the first time and being blown away because I had never heard anything like it!" You might consider another album you hear later better, but still consider that first one your favourite because of your personal experience with it (which has nothing to do with the quality of the music in isolation). Not everyone makes the separation but people that do aren't necessarily contradicting themselves.