Why are you using the pin out the way that you are?
I would think that it would be better to bring in the 3.3 at the top of the board on the opposite side. Same thing with the ground. Bring it in on the top and on the other side. Shorter runs. Slide all the signal pins down 2 positions.
Also, are you going to put screw holes on the board so it can be mounted?
Yes, it can be a problem with current and voltage requirements. The max voltage from a USB port is 5 volts. There are voltage drops in the H bridge. What about current? How much current does each motor take?
Turn the motors on with the program and measure the voltage across the motor leads.