Digging up an older thread, because is seems to be asking a similar question.
I have an Arduino Uno R3 + Arduino motor shield, and I'd like to power two motors AND use both of the external interrupts for encoder reading.
But pin 3, which corresponds to interrupt1 is used for PWM A on the shield.
So I don't see how I can do both. Is this correct? Is this what's causing the issues for the OP?