The bike should be of merchantable quality so you will need to get the dealer to ride the bike and make sure they accept there is an issue.
Suggest you get this done before you leave the premises.
If not done before you bought it then the least I would expect would be for the dealer to fit new plugs, oil, fuel and air filters and an oil change. Also a carb sync would be in order. That should ensure that the basics are correct.
Depending on the mileage then you could also ask for evidence that the valve shim clearances have been checked (every 40000 Km).
If it is running on three cylinders then you should be able to feel (without touching - that hurts!) a difference in exhaust temperature.
That could be caused by a bad plug, plug cap or lead. You could also check around the coil tower (I hope it isn't one of the front cylinders - they are a sod to get at) for cracking, burning where the lead fits in or corrosion.
Be careful not to loose the O ring that fit around the lead.
If it idles OK but one cylinder drops out once you start to add revs then check that the throttle slide of the offending cylinder is rising. Easily done with the Faux Tank and air-box covers removed. You will see the slide move up as the throttle is opened but it's not a good idea to do this whilst riding.
A compression (or better still cylinder leakage) test may also be in order.
I did have a DOH! moment when my bike developed a misfire which got progressively worse. Some incompetent buffoon (a.k.a. me) hadn't screwed the plug lead into the plug cap.