One problem related to manual transmission has been reported for the 2005 Mazda Miata. The most recently reported issues are listed below. Please also check out the statistics and reliability analysis of the 2005 Mazda Miata based on all problems reported for the 2005 Miata.
I purchased a used 2005 Mazda Miata 5-speed in April 2006 with 7860 miles on the odometer from the local Chrysler dealer. I had not driven the vehicle out of town until October 2006. On the interstate highway I noticed the vehicle had inadequate power to safely drive at the speed limit (80 mph). Top speed is only 82 mph @ 4200 rpm in fifth gear (should be 120 mph plus) and acceleration up a hill is bad. I must downshift and floor the accelerator to maintain speed up hill and the cruise control will not hold the speed. Trying to pass a slow vehicle uphill is almost impossible. The vehicle is in the local Mazda dealer's service department where they have not found the cause of the problem. I have had the vehicle serviced as required at the Mazda dealer and have even replaced the air filter when not required. This vehicle is unsafe to drive other than on flat, low speed, city roads.