I wouldn't really say that the Prometheus situation is anything comparable to this. Prometheus was initially born as a direct prequel to Alien, and it was announced as such. Then, at some point in pre-production, it started transitioning away from that "direct" prequel aspect, while still remaining within the universe and set prior to Alien, and Fox was very open about that, too.
The confusion there stemmed more from fans making a bigger deal of the term "Alien DNA" than they really needed to. From the marketing end, they were rather explicit about Prometheus' intentions.