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Hiya
We purchased a 2007 toyota wish about 3 months ago - all has been good. But recently, after parking near some trees ended up with quite a few bird droppings on the car. When hubby cleaned it yesterday he noticed a few patches where the clear protective coating had come off in a few places on top. Tiny patches - maybe a cm in diameter. Would the bird droppings have eroded the clear protective coating on top of the paint, or something else?

Bird droppings can be quite corrosive so it is highly likely the bird droppings have eaten into the clear coat. For this reason, it is most advisable to clean off bird droppings as soon as they're noticed.
I'd still suggest getting the opinion of a car painter, as if it's some sort of defect (eg; a previous repaint where the clear coat hasn't been applied properly), there may be a possibility that the dealer is perhaps responsible.