It *can* be seen as rude, depending on the culture. Like, "I did your job for you because you took so long". More often in "high class" settings, like places that need reservations weeks in advance.
But most of the time, people just don't care to assist the waiters and most waiters will appreciate it if you stack the plates. Some may judge you if you do it wrong.
Apparently I'm a truly good human because my organizational autism trait gets triggered. I'm not even annoyed fixing them. It's just satisfying to see them in order.