On some engines a sticking variable valve timing valve can cause the Check Engine light (MIL) to illuminate. Replacing the valve and a software update will address this issue.
Problems for specific Honda Civic years:
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Repairpal verified 2001 Honda Civic problems
CVT models (HX and GX) have a shudder, judder, and noise due to a worn start clutch in the transmission. Replacing the start clutch is needed to address this issue.