I'm sure you will get many opinions on this subject. 1st, I would assume you are not a gear grinder, so the metal shavings should not be a problem unless they continue, or get worse, at your 2nd fulid change. 2nd, if you have a 6 speed, I recommend you invest in one of Brian's Beatrush Shifter Collars. It will really smooth & tighten things up with your shifter. 3rd, and most important, change the tranny fluid to Red Line MTL, it should make a big differance for you. Let's call the MTL replacement, fluid change #1, so if you observe significant metal shavings at fluid change #2, then you may have a problem, but if so it will likely show up before you ever get to the 2nd fluid change. I would change the fluid every 12 months. Always drain the fluid while it is hot. My car sees A LOT OF TRACK USE, but it shifts flawlessly street or track, current milage is about 15k on the car, most of it on the track. The 1st time I changed the fluid was after owning the car for a month, I did it to solve the same problem you are having, never been a problem since. I hope this helps and you are better able to enjoy your great little car!
Pat- Va MX5
2012 MX5 PRHT GT