Hi friend,what do you think that have made people think they can't connect a motor with a photo interruptor on the same PIC?I think it's because they fear one of them will corrupt the other.Obviously it's the motor corrupting the photo interruptor.
Judging by the tune of the motor(or with the aid of a tachometer),did the RPM actually increase?You need to know it to determine whether the capture is working fine.If the RPM did increase while decreasing the duty cycle,then the photo interruptor could have no problem working with the motor,and you need to check the motor instead.
If the PWM generated voltage disruption did interfere with your photo interruptor,try reinforcing the isolation with optocouplers and better hardware to filter the supply for the photo interruptor.You can put anything together with a PIC as long as it makes sense.The only problem is how you get rid of the details.