If they are using a Y cable, they should of be receiving the same power and running at the same RPM speed. So the problem could be a manufacturing defect and you should contact the manufacturer if it under warranty. You can also open the case and verify if both cables are correctly plugged in the Y cable and in the motherboard fan header.
i just had a quick look and they seem to be connected to the cpu fan both, i dont think its a big issue though. aslong as they'll keep working ofcourse, i mean my Processor the I5 4690K isn't overclocked so the corsair watercooler is already overkill basically. it always runs on 30 degrees celcius on silent mode so its fine
feel free to add any advice still