A problem can occur with a vibrating expansion valve in the AC system which causes a whistling noise from the passengers vent. Replacing the expansion valve with an updated valve from Honda should repair this problem.
2006 Honda S2000 Problem Reports
RepairPal Verified 2006 Honda S2000 Problem Reports
The air/fuel sensor, located in the exhaust system, may be damaged by moisture in the exhaust resulting in illumination of the Check Engine Light. Replacing the damaged air/fuel sensor and updating the powertrain control module (PCM) software should correct this concern.
On certain models the PCM misinterprets data from the coolant sensor and causes the Check Engine light (MIL) to illuminate. A software update from Honda will repair this problem.
There are known convertible top issues.
There is an issue when the ignition switch is on for about four or more hours. The powertrain control module (PCM) can misinterpret serial data and cause the Check Engine Light to illuminate. A software update from Honda will repair this problem.