The problem with answering this question is that a lot of movies that in hindsight deserved many nominations weren't all that well-liked at the time, so they might not have been snubs then. Examples of films that are now "classics" but didn't get much praise at the time include Touch of Evil and The Searchers.
Steven Spielberg not being nominated for "Jaws," one of the most perfectly directed movies ever. There wasn't a single scene that, IMO, had a misstep.
The autopsy scene had one of the worst edits I've ever seen in a good movie. The infamous "This is what happens..." cut. He says it in the middle of the scene, and it's clearly part of a larger piece of dialogue, but that's all missing and the line has no connection with the lines before or after.