The Adventures of the American Rabbit
The towers can been seen around 58' and 1h07'.
*A Beautiful Day in the Neighborhood
Times are rough estimates as I saw the movie in theaters and didn't have a time stamp.
I've also heard that the documentary about Mr. Rogers (Won't You Be My Neighbor) talks about 9/11. I've never seen the movie myself so I can't confirm or give you any times.
*King Kong (1976)
Shot of WTCs at 1hr 42min and 1hr 43min
Shot at 1hr 20min
The Last Seduction has another WTC shot that wasn't on the list at 41min 36sec.
Rocketman (2019) has 2 shots of the WTCs. One day and one night shot both somewhere between 1hr 41min-1hr 43min.
There is a shot of the WTCs in the movie Us. Around the first 3 minutes of the movie during a Hands Across America commercial.
Also there is a missing shot of the WTCs in the movie It Could Happen To You at 1hr 37min