One problem related to engine cooling system has been reported for the 2006 Honda Pilot. The most recently reported issues are listed below. Please also check out the statistics and reliability analysis of the 2006 Honda Pilot based on all problems reported for the 2006 Pilot.
Condenser design on 2006 Honda Pilot. Condenser is easily damaged by road debris and not covered under warranty. I checked the internet and this is a common design flaw across all Hondas. The newer models have modified the grill to prevent debris damage to the condenser.