During the hotel room scene when the stuff is pushing the man up the wall, if you look closely where the two main characters are supposed to be standing and watching the event, you can see they are replaced by stand-ins, and only the characters' voices can be heard.
When Moe is threatening the two executives in the penultimate scene, he says, "Keep eating it till it's coming out of your eyeballs." In the next shot, Moe's mouth isn't moving as he finishes the sentence.
In the scene at the Stuff factory, they stumble across a room full of Stuffies dressed in yellow, lying on the floor. In the shot directly after Jason says "Whatever was inside of them must have just taken off," the camera pans around all of the Stuffies, who all have their mouths open and tongues sticking out. The actor at the top of the screen (the farthest from camera) is wiggling his mouth and tongue rapidly, indicating that not only he is very much alive, but quite likely didn't even hear the director's call of action.
Colonel Spears says that his radio station is based in Atlanta, Georgia (where his militia and he eventually broadcast the final warning). However, the signs on the wall of the station say WGHQ 92, a New York-based radio station, and the exteriors are of WBPM, which is in Kingston, New York.
During the Taste scene at the end with Patrick O'Neal, his character says, "We tested it. We tested it in a small Illinois Town." Between those two sentences, a car horn sounds off from outside the building.
When Rutherford's chartered plane is seen landing in Georgia, upon exiting the plane, the jet engines are heard winding down, but the starboard engine's fan is clearly seen to be stationary, meaning that the audio of a jet engine spooling down was added in post.