Do you encode with iTunes' error correction turned on?
Usually when I've double-checked, any faint "blips" that I thought I heard have actually turned out to be present on the original CD. That, or figments of my imagination/cases of me listening too intently and picking out something that sounds unusual on its own, but really isn't.
My copy of the Beastie Boys' "License to Ill" has routinely gotten mangled in rips, though. At least one of the encoded tracks will usually have period of loud, stuttering beeps. I guess it's just a bad pressing or something, because the disc itself is completely clean and scratch-free.