I can think of a number of years where the winner should not have won: 1980, 81, 1990, 2000, 2002, 2007.
Some of them I attribute to things outside the IFBB choices, Arnold when he won the show above picked the judges, because until 2 days before, no one knew he was going in the show. Word is that Joe Weider was very infuriated about the final result, same the next year, he was upset.
1990 I kinda understand what happened, this was the first show (and only) where it was drug-tested, and if you own any of the magazines from the time you were constantly reading how they were natural (even before the testing), so if the champ suddenly got beat when they started testing, it would make the entire organization, perhaps sport look bad, in the wake of Ben Johnson's positive test in 1988.
That same year Shawn Ray lost his Arnold trophy to Mike Ashley after having tested positive.
But you must remember how hard the IFBB was working in the early 2000's to try to make the judging more transparent. Unfortunately they decided to absolutely destroy the freeposing round in the process.