GPIO Controls but no USB

[rangersedge]

I'm using the Pi Zero for the Gameboy build. I didn't get a Teensy so I figured I would use the GPIO option. For some reason the USB hub will not work. The HDMI output doesn't seem to work either. I put the exact same card in a PI 3 and it all works fine (no GPIO pins used on this one though). Any idea why the GPIO would make the usb and hdmi ports stop working?