S.A.
I vaguely recall that young children think of pee and poop as part of their body, so seeing come out (and then flushed away) can be upsetting. Have you read books or watched videos like "Once Upon A Potty?" This might help your child understand what is happening, as it reviews body parts and also shows various scenarios such as sitting on the potty and nothing coming out, having accidents (on the floor instead of the potty) and finally peeing and pooping in the potty, then flushing it and saying "bye bye wee wee, bye bye poo poo." (My girls are older now, but I have read/watched that so many times that I'll probably never forget it!)