Which prefix is used in the word 'प्रतिकूल' (Pratikool)?

A prefix (उपसर्ग) is a letter or group of letters attached to the beginning of a root word to modify its meaning.
Breaking down the word 'प्रतिकूल':

$$\text{प्रतिकूल}=\text{प्रति (Prefix)}+\text{कूल (Root word)}$$

Hence, the prefix used is प्रति.