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My first mistake was probably letting Discount Tire touch my car (no offense to anyone that works there but this location seems to be bad as they've also cross threaded studs on my friends cars). After a rotate and balance they had managed to strip a wheel stud. And of course my steering wheel still vibrates @ 65+. I tried to get that fixed at another place but something is still out of whack (also hadn't had a problem with this up until this point).

The one place that I trust to work on my car, had to take the wheel hub off to get the old stud out and put the new one in. Ever since then I've had this noise whenever I step on the brake pedal (which wasn't there before). When I apply full force it doesn't make the sound, only with light pressure do I hear it. It doesn't make the sound while the mechanic is in the car. Two different mechanics have taken the wheel off to inspect the brakes. They said both times mechanically everything checks out. Anyone have any clues as to what might cause the squeak?

The only way I can describe the noise is that it sounds like something on the disc making a sound every time it goes around at a very specific point.

01 civic ex sedan stock

 
Rep Power: 319

Well, there is a chance your rotor is warped, not sure how that is related to all this though and that should give a pulsing in the brake pedal. Other than the fact that squeaky brakes is kind of a known problem with 7thgens, not sure what to tell you. Most people just live with it, as long as it doesn't get worse. Sorry, I don't have much advise

 
Rep Power: 296

if they took the hub off, then they must have taken the caliper off too. You might just need some antisqueek goop in the bolts, this happened to me when one bolt siezed up. Its worth a try, but requires u to disasemble the caliper. Oh and to add to that, put some antisqueek goop where the metal on the pads touches the caliper.

 
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sounds like the rotor has a high spot on it. or warped.

 
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If the rotor was warped wouldn't the brake pedal pulsate (it doesn't btw)? If the rotor does have a high spot on it, what do I do to fix it?

 
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all you have to do is have a REPUTABLE service station resurface them. They'll put em on a rotor lathe, and grind some of the surface off until its smooth and level. shouldnt take more than an hour if that.