Airbus narrow body OEB Bulletin 808/1 (Subject: FQI Accuracy) gives a good explanation of what may be happening. To summarise:
FQI accuracy is +/- 1% of max tank capacity or of actual fuel quantity
Bowser quantity (volume tolerance +/- 0.50%) & density error (+/- 0.25%) accuracies are 0.75% combined
APU burn on a 30 minute turn approx 30 kgs
FU indication accuracy (which is an integration of FF) is +/- 1.5%
Both on-ground and in-flight discrepancies are generally due to FQI errors on Block Fuel.
Notice the maximum Bowser error of 0.75% is potentially significant and if combined with the other inherent errors may offer an explanation.
Hope this helps.