Well i haven't heard of any such problems with the WagonR Duo...i guess both LPG as well as CNG as an alternate fuel have their plus points as well as negative ones. I can shortlist a few for you.
CNG:
You will notice a slight dip in power/acceleration i.e. about 10-15%
The CNG kit takes up a lot of space in your car trunk specially in a small car
A safer fuel than LPG since its liquefied gas (condenses when comes in contact with air)
You will notice a 50% increase in your Fuel efficiency..so the running cost is even lower than that of a LPG car
LPG:
There is no dip in engine power/acceleration
The kit is smaller in size so it helps to give you storage space in the car trunk
Higher risk since LPG is a combustible/inflammable gas
Not much change in car fuel efficiency figures
From a couple of people that i know of who have installed a CNG kit in their WagonR's from outside (since it doesn't come factory fitted) they're simply all praises for it. The car adapts to CNG so well & gives an average of 21-22 km per kg of CNG which is just Rs. 19.20 per Kg. So effectively the running cost is just 80 paise per km which is simply great saving & value for money.
I dunno the exact figures for the WagonR Duo...see if you can find them out...that ways you'll be able to do a better comparison.
The other option you could look at is the Santro CNG which is coming factory fitted straight from Hyundai's plant.