Nope, mine did that since it was brand spanking new.  I've noticed other members over the last year have made comments about it happening from time to time, with specifically the 1-2 / 2-1 shift.
The Savage's got a transmission with its own quirks just like other bikes do, I guess.  Besides the 1-2 shift grinding, you'll hear people post about the 4-5 upshift issue (with the newer bikes that have a 5th gear), getting the bike out of neutral when sitting still at a traffic light (for those who shift into neutral at a redlight - not me personally), and I'm sure there are other things too, I just can't remember at the moment.

-Pabst