You shouldn't attach a fan to the AIO_Pump header, that's not what it's for. That header is specially designed to attach SOLELY a liquid pump motor to, because that header ALWAYS needs/gets 100% power, regardless of setting. You need to connect the case fan to CHA_FAN that's what its (designed) for. A chassis (case) fan. CPU_FAN is as the name sais for the fan controlling the CPU, and AIO_PUMP exclusively for the motor of a liquid cooling system. It'll be in the manual too.
Page 1-13 of your manual:
Connect the pump cable from the all-in-one cooler (AIO cooler) to the AIO_PUMP header, and connect the fan cable to the CPU_FAN header. If your AIO cooler has more than one fan, you may need to use a pigtail cable to connect the cooler to the motherboard.
If you want to control more than 1 fan on CHA_FAN you'll need to use a fan cable splitter. You're using the header wrong, and asking something of it which it's incapable of doing.