Audio problem: Clark listens to his father and Earl talking in the hospital through the visitor window. The sound is the same volume and quality as when Earl was using the microphone, which he is not using now. Even if Clark used super-hearing to eavesdrop, it wouldn't sound the same as the microphone.
Audio problem: After Clark's parents come home, after their anniversary dinner, Jonathan and Clark go to see Earl in the hospital. As the Doctor says "It looks like he's got some sort of mineral poisoning, but its not from any mineral I've seen before." For the first few words of that line her mouth does not match up to what is being said but the dialogue, and her mouth slowly come together at the end of the line.
Audio problem: After he breaks the methane valve, Earl runs to the security camera and whispers, "You see what you made me do?" His whisper is heard at the proper volume by the Luthors watching the camera, but the speakerphone is on the desk ten feet behind Earl, making this impossible. Most surveillance cameras don't have microphones.
Revealing mistake: At the command center outside Martha is watching a monitor with the hostages on it and she asks "Where's Clark?". The next shot is one of Clark running down a hallway, inside the plant, using his super-speed. As he is running the red lights along the ceiling are revolving faster than they normally do and return to normal once Clark stops using super-speed.