These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Anvilicious: The final shot is of the New York skyline circa-1970s, including the World Trade Center.
Internet Backdraft: It was drowned out somewhat by the much bigger controversy over Brokeback Mountain that year, but Munich did have its own backlash from people who thought that the main characters were portrayed as "terrorists" and/or that the Munich perpetrators they were hunting down were depicted too sympathetically. Various pro-Israel groups organized boycotts of the film.
Narm: Near the end of the film, Avner seemingly has a vision/flashback/what have you of the deaths at Munich while having sex with his wife—this is the last of several such scenes in which Avner thinks about the events at Munich, despite the fact that Avner can't possibly know what actually happened, making it all a bit strange.