Visible crew/equipment: When the Overlord is busy destroying the Diner, when he starts destroying stuff on the counter, you can see the small rods pop up that flip the saucers and glasses into the air. You can also see the compressed air they used, to aid with the effect.
Revealing mistake: When Howard's running from the female bikers, Satan's Sluts, look closely at one and you can tell it's a guy in drag, one wearing a dark blond wig. (00:10:00)
Rob245Other mistake: In the scene where Howard falls asleep in Beverly's apartment window and his wallet falls out, she takes out the money. The city on the bill says Washington DC instead of Marshington DC. (00:19:00)
Continuity mistake: When the Overlord is about to explode the Ketchup and mustard bottles, the Ketchup cap is either loose or tight depending on the angle.
Sacha
Audio problem: When Howard's couch is about to be sent backwards he says "What is going on here?" but he's not mouthing the lines.
Sacha Continuity mistake: When Phil explains the ascent of duck, check Beverly's left hand: in some shots it is long enough to touch Howard's elbow, but in other shots her hand has shortened and it's by his shoulder.
Sacha Continuity mistake: In the angle shot from the side Phil holds the recorder with both hands, in the angle shot from the front he holds it with his right hand.
Sacha Continuity mistake: When Phil meets Howard he takes the recorder out of the pocket and takes it to his mouth. When the shot changes the recorder has vanished and he repeats the previous movements.
Sacha Continuity mistake: Howard falls through a ceiling and nosedives to the floor but a shot later he is falling butt first on the couch.
Sacha Continuity mistake: When Howard pulls up the microlight throttle the lab building is behind them. A shot later the building is gone and we see the gardens that the microlight passed by several minutes ago.
Sacha Continuity mistake: Before the microlight crashes against the banner the people gather on the road. A shot later the road is empty and people are gathering again.
Sacha Continuity mistake: Howard asks Beverly where he is and she extends her left arm to grab a bin behind. A shot later her arm is in front of her.
Sacha 
Revealing mistake: When the microlight is about to fall into the lake next to the lab, Howard's POV shows a straight road ahead. However, a shot later the microlight rises from an obvious ramp hidden between bushes which results in a more comedic crash.
Sacha Revealing mistake: When Howard climbs up a truck and fires the blast that destroys the laser, he is replaced by an obvious doll, not only does he not move an inch, but when the truck shakes he wobbles as if he was nailed to it.
Sacha Visible crew/equipment: When the cop commands Overlord to turn off the engine, filming crew and equipment are reflected on the front part of the truck.
Sacha Continuity mistake: When Overlord electrocutes the cop there's an driver watching everything horrified. His right hand is either lowered or on his face depending on the shot.
Sacha Revealing mistake: When the Overlord extends his arm outside the truck, lights up and electrocutes a cop his arm is not reflected on the truck, revealing it was a superimposed image.
Sacha Continuity mistake: After the duck hunters scene Beverly is inside the truck with her left arm raised. In the immediate next shot it's lowered.
Sacha Continuity mistake: When Howard and Phil's microlight is about to crash against the stall the people run away. A shot later two men have suddenly appear only to disappear a shot later.
Sacha Continuity mistake: At the nuclear plant, when the visitors walk around the place Overlord rests his hands on a glass but a shot later they're lowered.
Sacha 
Answer: He probably goes back to being a scientist afterwards. Maybe he went into hiding after what he'd been through out of fear of the government wanting to hold him responsible for that power plant's mess.
Rob245