Factual error: The alligator mentions wanting a Bananas Foster. This dessert was invented in 1951 but this movie takes place in 1926.
Other mistake: When the old woman is cooking gumbo in a large bathtub, it's shown boiling and really hot. Yet the two frogs can sit right on the rim of the bathtub inches above the boiling food in a non insulated tub without getting burned or even hot.
Answer: They physically left. Just because we didn't see it happen doesn't mean it didn't happen. It's a montage of their activities after they returned to human form.
LorgSkyegon
I thought as much, but it would have been even better to see a montage of them physically leaving the bayou and planning their church wedding.