Due to the area I live and my job, I spend more time working on my KTM than riding it. It is a big plus to me that KTMs are so easy to work on and well thought-out in design.
Due to the abundance of aluminum, a torque wrench, thread lube and Loctite are musts. Certain bolts like nothing more than to fall out. Seat bolts were my #1 flaw, losing two of them and those washers are pretty darn expensive... I will machine my own in the future :)
I have had shock bolts loosen several times... I safety wired them, so no more problems there. If you run your rear wheel far back for longer wheelbase, be sure to remove the adjuster bolts and lube them with anti-seize agent - they will get stuck otherwise.
I had a pipe break near the head flange. Bike was pretty old and KTM still replaced it.
You will have to jet the bike and may need a different needle to get it right.
Some people have had trouble with their seat covers - I have not - and KTM replaces them no prob.
Rear brake is grabby. I use EBC pads and that makes it easier to ride without lockups.
No other problems here except for setup issues.