It was probably Porter. He has nothing better to do since he's basically trapped in the train station. Heck he even writes a review when you're trying to get a perfect town. Culprit right there!
They actually don't grow everyday. It depends on whether a pitfall seed or not is already buried. If there is no pitfall seed in town, a new one will form the next day, just like fake rocks or fossils.
I remember when pitfalls use to be prank items that are hard to find in the GameCube Version. Now they're quite common and not as fun as they used to be.
I think it's the Resseties, not Don maybe but the other guy. He could be doing it since you does dig and is a mole. Maybe he gets rid of some anger burying pitfalls for everyone to trip in. Pranking anyone he wants.
At least in the GameCube game, they do bury them. Although you won't see them bury it of course. Last month, I found this on the bulletin board.
And when I went to that acre, sure enough, I found a pitfall buried there. And pitfalls are fairly rare on GameCube, so I'm sure it wasn't a coincidence. Besides, I didn't see any other buried items there.