Wallace & Gromit in The Curse of the Were-Rabbit: The eponymous monster leaves a Were-Rabbit-shaped hole in the church window during its first rampage. What's odd is that this outline doesn't match the silhouette of the Were-Rabbit when we finally see it.
The first Ice Age film does this thrice with a wall of ice, first with Sid the sloth going through and leaving his outline, then Diego the saber-tooth tiger, then Manfred the mammoth, resulting in a progressively bigger hole each time.
In Monsters vs. Aliens, after Ginormica gets captured by Gallaxhar, she escapes and chases him through Gallaxhar's spaceship. He tries shutting a series of doors on her, but she easily busts through each one, leaving a series of holes shaped vaguely like herself.
Near the end of Kung Fu Panda, Tai Lung leaves a perfectly Tai Lung-shaped hole in the ground after being belly-slammed straight up in the air by Po.
In The Iron Giant, Hogarth explores the woods behind his house and is shocked to find that the trees have been parted in the rough shape of a giant robot.
Disney's Alice in Wonderland. When the Walrus is running to escape the enraged Carpenter inside their shack, he runs right through the swinging door, leaving a Walrus-shaped hole.
In the original film, when the boys play Follow the Leader, they go under a waterfall at one point. Michael, The Runt at the End, jumps through it, briefly leaving a hole in the water shaped like himself and his teddy bear.
In Return to Neverland, when Jane fails to fly she falls right into the ground, leaving a Jane-shaped hole.
In Cars, Lightning McQueen leaves a himself-shaped hole in the smoke when he leaps over the wreckage in the first race.
In Cats Don't Dance, Danny leaves such a hole the floor when Max drops him from such an extreme height.
In Chicken Run, Ginger and Rocky try to escape from the oven of the pie machine, but Rocky keeps stumbling around and falling into all of the pies in the oven, with all of the pies having Rocky-shaped holes in them.