Monitor your koi carefully for signs of Parasite infections and exercise proper quarantine procedures are critical for maintaining a healthy pond ecosystem. Most parasite treatments cannot be used in cooler water temperatures (<50 degrees). Unfortunately, it's also these cooler water temperatures when the parasitic infections are most commonly discovered because the koi's immune systems are too weak to fend them off.
Close monitoring, skin scraping, and early treatment for parasites when first discovered are key. Keeping your water pristine during your treatment period, through frequent water changes and testing and the use of beneficial bacteria will help prevent secondary bacterial infections and/or fungus from making things worse.