Yes, the aircraft fuel gauges are normally very reliable. However there are any number of situations that might cause a discrepancy. Those discrepancies can range from technical faults, to simple human errors such as what the last crew wrote in the technical log, or a refueller writing a 9 that looks like a 7. There are a series of checks that are applied to every refuelling operation that, within defined margins of error, should safeguard against gross errors. When these checks throw up a discrepancy it is obviously important that the discrepancy be resolved before the crew can sign off the refuelling log, and the captain can then sign the tech log.
Aircraft can (in defined circumstances) dispatch with an unserviceable fuel gauge, but it is clearly important that the fuel on board is confirmed prior to dispatch. The tank quantities can be read by mechanical "sticks" prior to dispatch in order to confirm quantities and it would require other measuring systems be fully serviceable.
The basic check is that the crew calculate what they consider the fuel uplift to be. The actual uplift (for many reasons) is likely to vary from that figure, but should normally fall within a limit of 5% of the calculated figure. If it doesn't then further investigation is almost certainly warranted. The likelyhood is a human error in paperwork entries or mathematical calculation, but the gross error check is also a line of defence in more serious potential issues such as leak or faulty equipment.
Most aircraft systems are very reliable most of the time, but the system redundancies, and most importantly the cross checks are in place to ensure that reliability isn't taken for granted. Most of the time a discrepancy can be properly resolved quite quickly, but irrespective of how long it takes, it is vital that it is properly resolved.