In the first episode Toad's costume is different, his hat is red with white spots instead of white with red spots. It's been established the cap on his head is a hat so he simply changed clothes.
However, he has never done anything like that again, making it more likely that it's just a case of Early-Installment Weirdness.
In "Do You Princess Toadstool Take this Koopa...?" King Koopa turns Toad and the other Mushroom Kingdom Denisens to stone to get Princess Toadstool to marry him. While he later reveals he has no intention of changing them back permanently and turns them to stone again in an area the Princess doesn't see, the Mario Brothers eventually manage to turn Toad back. The rest of the inhabitants are still stone though, and the wand used to change them is destroyed. We never even see them changed back.
Whenever you stomp on a goomba, you could be stomping on an innocent kid who didn't watch the Super Mario Bros. Super Show.
