When George rescues Harry in downtown Seattle, you can clearly see that the roof of the station wagon is pushed up, from earlier when Harry got in. But when he gets in this time, you see the roof getting pushed up again.
Harry crashes his head through the Hendersons' ceiling, but in the next scene it's undamaged.
As the family is driving through the woods before hitting Harry with their car, the sun bounces back and forth from high noon to late afternoon. The sun is in George's eyes when he hits Harry but the sun is directly overhead in the shot just before.
All of the baby pigeons roosting on Harry's shoulder just disappear a few seconds before he jumps out of the tree.
In the city when George finds Harry in the dumpster he drives the trash truck away and just before Lefloure pulls the trigger on the gun, George stops short and the dumpster goes flying. The dumpster flips over, top down and sparks fly, but in the next cut the dumpster is top up again.
When George aims his rifle at Harry through the upstairs window and looks down the scope, the image of Harry is clear. With the target that close, the image would not have appeared that clear and sharp but would have been heavily blurred.
George tells Wrightwood to take the I-5 into town from Index, but I-5 doesn't go anywhere near there. He should have said to take I-90.
When Harry roars through the windshield of the car before being thrown off the roof, Kevin Peter Hall's own mouth and teeth are visible inside Harry's mouth.
When Ernie tells his parents that Harry "...didn't like the blue-cheese." and the camera shows the wall, it is obvious the dip had already slid down on the wall in previous takes.
The Hendersons' station wagon is clearly already damaged in the close-up of it hitting Harry. The headlight cover is already open instead of coming open in the crash, and damage to the left front panel is grossly exaggerated and inconsistent with hitting Harry the way they did. It also looks like the license plate is already off of the car while hitting Harry at the same time.
On the freeway, all of the vehicles in the first shots of LaFleur speeding towards the Hendersons in George's station wagon are stationary, despite many of them being way back before the impending traffic jam with huge gaps between them.
At the end, when Harry is going back to the forest, the dog can be seen barking but no sound of barking is audible.
The side of Ernie's face and the steadiness in his speech shows that Joshua Rudoy's voice was added in later when he runs to get the camera in the closet.
The exit sign that leads to Mt. Rainier actually goes to Lake City Way in real life. The actual exit to Mt. Rainier at that time was ugly with construction during the filming of this movie.
George's father tells him to "stick a pin in Queen Anne's Hill"... It's actually Queen Anne Hill.