Well, not if you're doing it right.
If you're squatting properly, squatting below parallel can actually reduce the stress on you knees. According The Hartmann et al study, squatting above 90-degrees can actually can actually strain your knees.
Squats (low or high depth) can cause injury if you're not really careful. It's important to remember that if you do intend on squatting below parallel, that you keep your form unbroken. Personally when I was powerlifting, I found that a high bar, deep squat worked best for me. If you do intend on squatting low, I'd suggest wearing squat (weightlifting) shoes, or placing plates under your heel. Your heels may raise, and having the support under your heel helps stabilize your position. Just remember, flexibility and balance plays a part as well.
My best advice? Do what works for you. You can do a low-bar squat or a high-bar squat. You've got options!
Deep squats bad for you? Only if you think greatness is bad for you...