Beats me... I have just over 400 miles on mine, and I don't have that particular issue.
I think you may be taking the shifter into 3rd gear a little
faster than the clutch pedal being depressed properly...
When I first learned how to drive a manual on my Evo, I remember myself encountering similar obstacles... I suppose it comes down to practice, and also better understanding / learning the specific car's shifting and behavior.
Please feel free to correct me if I've mistaken.
