One of my favorite bloggers, Joe Posnanski, breaks down the climatic scene where Indiana Jones and the bad guy have to choose the true Holy Grail. As with all of his posts, this one is excellent.
So … did Elsa purposely give him the wrong cup? I asked this question on Twitter, and I would say 90% of people say yes, of course she did. She wanted the grail for herself. She had become disenchanted with the Nazi philosophy. She had feelings for Indiana Jones and for his father (who was dying in the other room waiting for the cup to be retrieved). After all she gave Indiana Jones what could be described as a knowing look.
Except, may she didn't. Read more here.