Signs of a Bad Honda Fuel Filter | It Still Runs A clogged or damaged fuel filter will disrupt the flow of fuel into the engine block. The car will hesitate, or the engine will sputter during acceleration. This can be accompanied by a shake in the Honda's body--in particular with Civics and the CRV (which was built using the Civic chassis), which have predominantly all-fiberglass frames. Honda 5 Symptoms of a Bad Fuel System | Honda-tech Mar 13, 2015Honda: 5 Symptoms of a Bad Fuel System. A bad fuel system does not have to cost you your Honda Accord or Civic. Learn the simple repairs you can do right at home, and which ones are best left to a professional.