Tried one and two 0.1uF caps between the motor terminals, noticed some improvement but usb still stops working eventually..
Did you mean caps from the motor terminals to the ground as well? I don't have enough here to do that today :/
I'm getting suspicious of those pull-up 1k resistors between each input terminal and 5V, could they be providing a path for supply interference to affect the logic wires? I'm not even sure why those resistors are there, most L298N circuits don't have them at all.
The motor supply is already isolated: 2x16340 for motors and USB for the arduino - unless you mean using a third supply for the logic part of the H-bridge board. I only got this board because it was supposed to "just work". One or two caps are fine but if I have to add a lot or even opto-isolators it's certainly not worth the trouble...
Edit:
As a side note this motor is one of those very small radio controlled toy car's.
All the interference is gone if I wire a diode in series with the motor but then I obviously lose the other direction..