Both capacities stack
The Crippling Critical ability states that:
When you confirm a critical hit using a light or one-handed piercing weapong, you can apply one of the following penalties [...list of possible penalties...]
These penalties last for 1 minute, except for the ability damage, which must be healed normally, and bleed damage, which continues until the target receives magic healing or a DC 15 Heal skill check.
The Critical feat special caveat states:
You can only apply the effects of one critical feat to a given critical hit unless you possess Critical Mastery.
The restriction is aimed at critical feats. Crippling Critical is a class feature, and nothing in it states it counts as a critical feat regarding the critical feat caveat. Therefore, nothing stops you from using both on the same critical.
Possessing Critical Mastery would allow you the base "critical feat + Crippling Critical class feature" combo and add an extra critical feat to the mix.