The Bengal cat is a fabulous cat having in abundance all the characteristics of the domestic cat. It is said that about 12.5% of wild Asian Leopard Cat (ALC) remains in a 4th generation (Stud Book Tradition) Bengal cat. So there is some wild in him. That is what you want. In fact some people like their cats to be more "wild" than that and consequently adopt a first or second generation cat.
One characteristic of the ALC is that she likes to defecate and urinate in water to cover her tracks. Sometimes this trait carries forward through the generations to an SBT cat. The Bengal cat has a propensity to go to the loo actually in the loo (or sink or shower for example) rather than the usual litter as a reflection of this characteristic.
It occurs to me that you might use this to advantage and train your Bengal to use the toilet properly like a human (quite a lot of people do this).
However, you can train a Bengal to use the litter. But in the meantime treat it as something that goes with the territory of a hybrid cat with some wild left in him.