One problem related to body has been reported for the 2008 Mazda MX5. The most recently reported issues are listed below.
When it rains water will pool in passenger side floor board. Mazda deals suggests adding drains and filters that are not part of original vehicle design. (this issue is due to a design flaw and no other reason), this happens regardless if car is moving or stationary. This has been an on-going issue since I purchased the vehicle in 11/2012. . Door seals and window seals are not damaged.