Backfeeding Power?

I plugged a led / motor power circuit into my breadboard last night and used a TIP31a/TIP32a to drive a 24v 4A pwm channel. Separate 5v power supply to the arduino (also tried usb) and it seems like the power backfed through the system and overloaded things. Only the ground from the arduino is connected to the large power as it wouldn't work otherwise. When I removed the arduino power supply and turned on the large supply the arduino powered up anyway. Am I missing something? It was only on for a few seconds because if it is powered up through pin 5/ ground from the large supply then it was getting 24v! Isn't a fet supposed to keep the two separate?

If done right, it should keep the power separate, but if not...
Also, they are not fet, just "normal" bipolars. Post the schematic for them.