The idea of playing the national anthem at domestic sporting events is generally seen as a pretty odd American habit. Which kind of reduces the scope for controversy to begin with.
I don't remember any
domestic controversies around the Swiss one ever; but that's simply because it's not generally perceived as a particularly meaningful national symbol. They even tried to change the words a few years ago, and that basically died as a project because no-one even really worked up the energy to worry about it. The fact that basically no-one knows what comes after "Sur nos monts quand le soleil, annonce un brillant réveil" is basically something of a running joke.
Although that said, the Serbian fans did whistle it at the world cup - but that was mostly understood through the lense of ex-Yugoslav politics (which kind of says it all, really). And even then, it was
something else that actually wound up creating the controversy; while the bit with the anthem was largely forgotten.