Though Muni fare inspectors tend to be miserable, grumpy people who do not want to hear your stories, there is in fact reason to argue that Clipper Card-based tickets might not be valid. As SF Examiner reports, card readers aboard non-Metro, above-ground vehicles like streetcars and busses don't actually acknowledge your payments until the driver's shift is over, which may not be for hours. Thus, if an SFPD officer comes aboard a bus doing a routine check for crime and fare evaders, he or she can't properly check your Clipper Card without a handheld reader, or without going to a device located by the driver's seat in which they can see any recent use of the car via a swipe.
S.F. resident and Muni rider Daniel Persson found this out one morning last month when he was issued a ticket by an SFPD officer after he had just made a valid swipe of his Clipper Card moments before.
As for tagging your card on the underground Muni, well, that supposedly registers immediately on your account. But this system is full of holes, people! And those trains have made you late for work or for appointments more times than you can count! Don't let them push you around if you swiped it somewhere and something went wrong and who knows?! Stranger things have happened. Here are some various ideas for fighting a citation by way of a hearing.