Andy -
Like Glenn said, if you're doing the CA WOD with real back squats and correct pulling/DL posture, yes, this quad/PC imbalance will correct itself. If it's really bad, consider doing only front squats, i.e. replacing all back squats with fronts for several weeks.
Also like Glenn said, there are a few possibilities for your problem - weak quads, crashing bar, being forward during the lift from the start, etc.
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