Any discrepancy will immediately show and proper analysis should resolve and indicate where the problem most probably is i.e. whether it is a fuel leak or indication problem, etc.
Not necessarily. Unless a dip is taken prior to each flight, an inaccurate fuel gauge can go undetected for some time. Say a gauge is indicating 500kg too high. The 3% check from the last flight was OK. The 3% check after refuel for the next flight will still be OK.
I have been caught by this once. Thinking we were going to land with what we wanted, on taxi in, one of the low fuel lights came on. Got the Engos to dip the tank - sure enough, it was way down on the indicated quantity and had flown for many sectors like that. Only when you "press the point" to minimum fuel will you find the error...unless you dip the tanks prior to each departure (which, it seems, QF decided to stop doing on the Classics) or after arrival.