Like with The Muppet Show, producers, directors and performers tried to make sure that the puppet characters of Muppets Tonight were presented as living objects. However, the occasional goof would appear, like those below.

Opening Theme

"Muppets Tonight Theme" Summary
MT opening goof 1
In the opening moment where Clifford begins to sing, the man performing Quongo can be spotted beneath him.
MT opening goof 2
The arm sleeve for the performer of Lew Zealand can be seen as he follows Clifford down the halls. In the same shot, the head of his puppeteer pops up.

Season One

Episode 101: Michelle Pfeiffer Summary
MT cheese goof
The hand of the puppeteer holding up the first cheese of Francois Fromage and his Dancing Cheeses can be seen as it enters.
MT nurse goof
In the scene after the Bay of Pigs Watch sketch, the sleeve of the puppeteer for Statler and Waldorf's nurse is seen as she walks off.
MT elvis goof
The puppeteer of the Elvis on the far left side of the screen during the Blue Suede Shoes number of Great Moments in Elvis History can be glimpsed beneath it.
Episode 102: Garth Brooks Summary
MT longhorn cheddar cheese goof
In the cold opening, the arms of the puppeteers of the Longhorn Cheddar Cheeses are seen.
During "It's Not Unusual", one puppet's arm sock can be seen in one shot.
Episode 104: John Goodman Summary
MT 104 cold open goof
When the unnamed Whatnot peaks into the room where Andy and Randy Pig have just been turned into bacon, his performer's arm sleeve can be seen.
MT 104 clifford goof
As Clifford enters the stage to open the show, the top of Kevin Clash's head, as well as his headset, can be seen popping up and down behind Clifford.  
MT tales goof
When the scene cuts from Dr. Phil Van Neuter yelling "TALES FROM THE VET!" during the Tales from the Vet sketch, either Brian Henson's or Bill Barretta's head pops up from behind him.
Episode 105: Cindy Crawford Summary
MT105 goof
As Clifford enters the stage to open the show, the top of Kevin Clash's head, as well as his headset, can be seen popping up and down behind Clifford.
MT105 cheese goof
During the Irish Rodents' song, a puppeteer's hand and head can be seen at the bottom.
MT105 AndyRandy goof
During The Eagle's Nest, when Randy says "Okay", Andy's mouth moves.
MT105 Bobo goof
During the tango scene, Bill Baretta's head is visible below Bobo.
MT105 Stu goof
At the finale, Stu, matted into the shot, fades out for a split-second as he comes onstage.
MT105 Sal goof
During the epilogue, Brian Henson's head and hand can be seen below Sal coming off the elevator.
Episode 107: Sandra Bullock Summary
While the Snowths are singing "Phenomena", a performer's arm can be seen.
MT 107 goof Rizzo
A finger and hand can be seen below Rizzo in one shot.
Episode 108: Jason Alexander Summary
MT 108 goof strawnose
A puppeteer's head is briefly visible below the straw-nosed creature.
MT 108 cannon goof
When Gonzo rubs the laser cannon during rehearsal for "Bats", Dave Goelz's head is visible.
MT muppet bandstand goof

MT muppet bandstand goof 2
During the Muppet Bandstand sketch, the top of Frank Oz's head is seen covered with a blue cap. A few seconds later, Miss Piggy's arm sock is briefly visible.
MT 108 ending goof
Several puppeteers' heads are clearly visible under the chickens at the end of the "Bats" number. They, as well as the chickens' arm sleeves are also visible during the goodnights along with the top of Kevin Clash's head.
Episode 109: Whoopi Goldberg Summary
MT 109 cold open goof
During the cold opening, a puppeter's hand is seen controlling Clifford's arm rods.
Episode 110: Martin Short Summary
MT ed grimley goof
During the Ed Grimley sketch, Frank Oz's hands are seen controlling Miss Piggy's arm rods.
MT 110 goof whatnot
The top of Frank Oz's head is briefly visible as he operates the one-line Whatnot.

Season Two

Episode 201: PrinceSummary
MT 201 stiff neck goof

After the Muppet Hoo-Haw sketch, Kermit rubs his stiff neck. Steve Whitmire's hand can be seen controlling Kermit's arm-rod.

Later, as he is leaving the scene, most of Kermit's arm-sleeve becomes visible.

Rizzo's arm-sleeve becomes visible when Prince tosses him off his shoulder.
Episode 202: Rick Moranis Summary
When Lash Holstein crashes into the house, his arm sleeves can be seen.
Episode 206: Paula Abdul Summary
MT 206 goof Paula
During the opening scene, one of the background Whatnots can be seen watching Paula and Clifford. If you look closely, you can see part of the arm of his puppeteer.
MT 206 goof cannons
Dave Goelz's head is briefly visible as Gonzo fires the cannons.
Kermit arm-sleve is seen at various times on the episode.
Episode 207: Dennis Quaid Summary
The top of Steve Whitmire's head is seen under Rizzo in backstage.
Episode 208: The Cameo Show Summary
Bill Barretta's arm can be seen under Bobo after "killing" Arsenio Hall.
Episode 210: The Gary Cahuenga Episode Summary
Kermit's arm-sleeve can be seen as he introduces the opening number.
Kevin Clash's head can be seen as Clifford faints.
Episode 211: Andie MacDowell Summary
As Kermit sings "Dancing in the Dark," part of Steve Whitmire's head, arms, and Kermit's arm rods become visible.
Episode 212: Johnny Fiama Leaves Home Summary
When Johnny leaves the room during the cold opening, Jerry Nelson's head is visible under Johnny Fiama's Ma as Zippity Zap's Mom follows her around the room.
Just before Ma whacks Sal, a the very top of a puppeteer's head (most likely Brian Henson's) is visible between Sal and Ma. Seconds later, a puppeteer's hand is visible when Ma whacks Johnny.
During "The Eagle's Nest," the top of Frank Oz's head is visible.