pepboys overcharging.causing damage and charging me for it.no information/no knowledge las vegas, Nevada

i took my car to pepboys because the alternator has stopped working while i was driving to an interview. they had ran a diagnostic on the vehicle and on that diagnostic everything else checks out fine. they intalled a pb/prostart platinum 85amp alternator inside my car(thats what it says on the diagnostic). a few days later i call them because they dont ever call me back when they say they will and they told me "when we installed the alternator sparks flew from the PCM.they said i would have to pay an extra 550 to replace the pcm.idid  not cause this damage and am not paying for anything except the alternator+the labor. everything comes up to $1372. thats ridiculous!..my car has been there since oct 15th 2010 and everytimei call back its always a different story.and the manager there (george ramirez) is trying to cover everything up.one of the guys that work there(erik) he told me 2 weeks ago that its the shops fault because once they installed the alternator the pcm blew.now they are trying to say that they never said that..and i have witnesses that heard everything..tell me they are not trying to scam me,or take advantage of me?