“. . . at/in the ending of the movie”

They all mean different things. “At the end” is chronological: the protagonist died at the time the movie ended.

“In the ending” has to do with the plot. In the ending, the protagonist fought mightily to defeat Godzilla and lost. He went out in a blaze of glory, much to the amusement of Godzilla who laughed loudly.

Now, you might say that the audience laughed loudly at the ending because it was so ridiculous. (In this case, “laughing at” the ending has the same context as laughing at a joke.) On the other hand, if you were to say that the audience laughed loudly at the end of the movie, it could be for any reason, not necessarily having to do with the movie itself.