I have two voltage sources. The first one is 230VAC to 5VDC cell phone battery charger while the another is output from Raspberry Pi's Ground and 3V3 pins. I feed the 5VDC output for an Arduino. What I am planning to do is to connect RPI's Ground pin to the corresponding pin of the 5VDC's Ground pin. That's how I would make a reference 0V voltage for data connection between RPI and Arduino. I don't have a voltage level shifter (these allow two different Ground references to be used) to do that easily.
However, I measured a voltage difference of 0.06 Volts between the Ground pins. I think it's little, but where does it come from and is it safe to connect the ground pins? I measured voltages between RPI's 3V3 pin and 5VDC's Ground pin, and vice versa and results were similar in these situations as well.