Filmmaking is an innately collaborative process: the director is normally the creative face the public get to see, but behind that you have producers keeping studios happy, writers trying to give something meaning and catering staff dealing with obnoxious actors. Everyone's important. Until the film is a success, at least. If the critics adore it or audiences just can't enough, the director is immediately ascended to the level of genius, maybe bringing a heavily-involved actor along for the ride.
Awards notice occasionally give the smaller players a chance to shine, but for the most part it's an individual heaped with praise for the group's work. Likewise, when a film fails, you can guarantee it'll all be made out to be the fault of one person. More often than not the director's the unlucky one, but the honour can realistically fall on anyone not quick enough to distance themselves from the project.
Most of the time it's justified - no one has shed a tear watching John Travolta spend over a decade trying to recover from his pet disaster Battlefield Earth - but sometimes a bystander to the whole thing becomes the poster child of failure. Normally it's the fans, hungry for blood that a promising idea was ruined, who pick their victim. And sometimes they get it wrong, like in these ten cases, where a movies failure wasn't (all) the labelled person's fault, despite what everyone said.
Who Else Was To Blame: Ridley Scott.
After a first viewing of Prometheus, fans quickly found the root of the Alien prequel's problem; its major scripting problems. But the screenplay wasn't all Lindelof's; the project originated with Ridley Scott and had its early drafts written by Jon Spaihts. It was at this stage that much of the plot's overarching themes were nailed down; the engineers, their creation of humanity and plans for destruction were present from the start. It was only when Spaihts struggled on a later draft that Lindelof came on board, where his big influence was reducing the prevalence of references to the Alien series.
Lindelof made some fan enemies (fanemies?) with the ending of Lost, where he and co-writer Carlton Cuse didn't info-dump the answers on the audience, even though all of the solutions are there though. Thus when Prometheus had a similar approach, leaving the motivations of the engineers ambiguous for the sequel (which ultimately bypassed this), people assumed that was all him. Though Lindelof certainly made some questionable changes, you can't blame the whole thing on him.