Due + PWM + Interrupts

I'm trying to control an Scorbot by an Arduino Due and H-bridges (L298N), the arm's motors have encoders which are readed by the arduino Interrupt function. Everything have worked well. But when I tried to involve PWM signals to move the motors, electrical noise gets into the interrupts and reads incorrect values.

I've tried isolating the H-bridges ground, feeding the encoders with an independent voltage source and connecting capacitors to the source, but the electrical noise keeps appearing. I've also tested with distribuited control through another arduino.
Please help, or comment if you have had a similiar problem.

which Due interrupts?
what is your code like?