It really only takes one or two shanked 1-2 shifts at WOT to bend a fork or remove some material from the gear dogs/pockets. It happens. Also, the rare but possible false neutral and trying to get it back into gear in traffic, etc. happens. And as Wfooshee mentioned, it's a progressive problem. It's not necessarily confined to one manufacturer of bikes, all bikes with sequential manual transmissions are susceptible to this problem. The more powerful the bike, the more likely for it to happen. We're talking about A LOT of power being controlled with an error prone human foot in the mix. I still have yet to hear of an AE bike with mechanical transmission issues.
I'm the unicorn of the forum who has split his motor twice to fix 2nd gear, the first time with new gears and a better condition fork, second time with all new, and I had sent 2nd gear set out to APE racing for an undercut.
Here's what I learned: Preload. When you preload the shifter during upshifts, you'll find that simply pulling in the clutch is enough for the gear dogs to engage smoothly. I was doing it wrong, thinking the best thing to happen was to stab it quickly with my size 13 steel toe boot, which is only partially correct. Quick shifts are a plus, quick shifts without preload ...aren't. They don't tell you that in the manual, they only convey that you should be shifting at low rpm/power/speed to cover their ***** for warranty claims. I learned to ride 8 years ago on an 800 lb. Royal Star with a heel toe shifter; it wasn't much of an issue on that bike.
I also gained valuable knowledge about the bike by pretty much gutting it twice. Second time around she got a new suspension because it was convenient at the time. (Seriously consider it if you've got the coin)
If you've got a mechanic you trust, that's fantastic. But I'm not sure I'd want to leave such a task to just any mouth breathing ***** with a wrench.
As ionbeam mentioned, you're probably SOL with a warranty claim, but I do wish you luck. If you're mechanically inclined and have a modest tool collection, you can pull it off yourself for under/around $4-500 bucks. But realize that you're in for a lot of work, and patience is valuable. Nothing too complex or challenging, just lots of things to do. Do lots of reading on this forum, it's been documented with pictures a few times.
Or you can sell it cheap to someone willing to fix it and pick up one of those sweet '16s next spring.