This will seem odd, but keep reading because I have seen a similar error before. I want to know details of what you are plugging in where.
You say, "their are 2 connections. One is a 3pin fan and the other is a molex but every time I plug the molex into peripherals + SATA ...." I wonder if you mean this: There is a cable included with the case with one 4-pin male (with pins) Molex connector on one end, and two 3-pin female (with holes) fan connectors on the other. You have plugged one or both female fan connectors into mobo fan headers and then plugged the Molex into a power output from the PSU. Is that right?
If yes, then that is the problem! That cable is used for something completely different! It is NOT ever supposed to be plugged...