I went here about six months ago or so to get my brakes serviced, and part of the package purchased included a tire rotation. Last month my car started shaking, and I thought there was a bubble in the tire. Pep Boys was going to charge $50 just to LOOK at my tires and see if it was a problem with the tire or the alignment (and that doesn't include any repair services). I took my car to a shop next door where they looked at the tires for free and it turns out that my tires had NEVER been rotated - and that I had a bubble in my front left tire. Shortly after replacing, my front right tire separated. These tires would have lasted months and months longer if I had actually received the tire rotation that I paid for. I still have my receipt from the service at Pep Boys and it was definitely listed on there.
They have also misdiagnosed things several times; last year I took my car in because it made a squeaking noise when I braked and I figured that I needed my pads adjusted. I was told that a wheel bearing was loose and that I was going to need a $500 repair in addition to the pad adjustment. I responded that I was just going to take my car to the dealership since that would be under warranty and have the adjustment taken care of there too. Suddenly they were mistaken and the wheel bearing was fine, all I needed was a brake pad adjustment.
They will overcharge you for services that most other places will do for free, won't actually provide you with the services that you pay for, and a lot of the employees don't seem to actually understand what they're talking about.