Usually popping on accel is indicative of an exhaust leak. The Ninja 250 has CV carbs which are basically vacuum operated. When trying to crack the throttle wide open there is a slight delay in response, especially in the lower rpm range.
Other than the popping does the bike drive OK?
Of course you know the Ninja 250 is a carbureted bike and carbureted vehicles have a hard time adjusting to temp changes unlike EFI. So instead of the engine having the right air-fuel ratio for the temp condition, the temp needs to change for the right ratio and proper combustion.
When the Ninja 250 is cold it doe not like a lot of abrupt throttle inputs, so you may notice some sluggish throttle response.
The amount of time it takes for a engine to properly warm up depends on several factors especially in a carbed engine. (fuel used, altitude, ambient temp, humidity and tuning) Every bike and situation is different. Today it may take 5 mins. to warm up, tomorrow it make take 8 mins.
The best indicator that the engine is sufficiently warmed is when it is able to idle steadily at the point in which it was set and is able to pull smoothly just off idle.
Most carbed engines, even when warmed, will not idle sewing machine smooth. There will almost always be a slight variation, bump or hiccup here or there, especially on fuel systems that are gravity feed (such as the ninja 250).
I would check to make sure you don't have an exhaust leak around the exhaust manifold (there have been incidences of those bolts vibrating loose).
If you think the bike is truly misfiring, it may be an electrical problem. Be cause you have so little miles, you may then want to take it to kawasaki and immediately have them fix it if it is still under warranty.
If you want to continue troubleshooting, here are some other things that may help pin point the problem.
Poor Running at Low Speed:
Battery voltage low
Spark plug dirty, broken, or maladjusted
Spark plug cap or high tension wiring trouble
Spark plug cap shorted or not in good contact
Spark plug incorrect
IC igniter trouble
Crankshaft sensor trouble
Ignition coil trouble
Fuel/air mixture incorrect
Pilot screw maladjusted
Pilot jet, or air passage clogged
Air bleed pipe bleed holes clogged
Pilot passage clogged
Air cleaner clogged, poorly sealed, or element missing
Choke plunger stuck open
Fuel level in carburetor float bowl too high or too low
Fuel tank air vent obstructed
Carburetor holder loose
Air cleaner duct loose
Spark plug loose
Cylinder head not sufficiently tightened
No valve clearance
Cylinder, piston worn
Piston ring bad (worn, weak, broken, or sticking)
Piston ring/groove clearance excessive
Cylinder head warped
Cylinder head gasket damaged
Valve spring broken or weak
Valve not seating properly (valve bent, worn, or carbon accumulation on the seating surface)
IC igniter trouble
Carburetor not synchronizing
Vacuum piston doesn’t slide smoothly
Engine oil viscosity too high
Drive train trouble
How Constant Velocity Carburetors Work
Motorcycle Carburetor Theory 101