I used to think that Sweetums was a bad guy, mainly due to his scenes in The Muppet Movie and The Great Muppet Caper, where he's seen running, yelling, and suddenly bursting through things. Even though he obviously wasn't bad before he started chasing the car. I also thought that the other mosnters were bad guys as well.
I thought that the monsters who look like birds (Boppity, Gloat, etc.) were "monster birds" (a name I made up myself for those types), and also thought that Fletcherbird was a monsterbird, due to the fact that he was a full-body Muppet and the monsters were full-body (and yes, I was aware that Big Bird, Snuffy, and Bruno weren't monsters, but they're from Sesame Street, not The Muppet Show).
I was unsure as to whether the full-body and hand puppet versions of Mean Mama were meant to be the same character or not. Ditto with blue-beaked Boppity and yellow-beaked Boppity. Not really a mistake, just something I wasn't sure of.
I thought that Thog's name was Donnerd. Mainly due to a line in Lorretta Switt's "I Feel the Earth Move" which I also mistook; When she said "Darloing, I can't stand it, when you look at me that way..." I thoguht she said "Donnerd" instead of Darling. And thought she was referring to Thog. Also due to that number, I thought he was a giant all the time. When watching that in "Rock Music with the Muppets" and then seeing "School's Out for Summer" later in the video I was surprised to see Thog be so much smaller, and wondered if he coudl grow and shrink on command (hmm, maybe that'd explain why the new Thog looks so much bigger in those on-set photos of the new movie).
Back when I didn't know Timmy Monster's name, I thought that Timmy's name was "Fruit Pain", and thought he got a pain in his brain whenever he ate fruit. I don't know why I thought all this, just made it up to myself (well, I thought the "fruit" parts were because hsi lips looked a bit fruity).
Thanks to Sweetums only being introduced as a "Jack" and not by his name I thought Sweetums was named Jack. When I first noticed the name "Sweetums" listed in the credits to The Great Muppet Caper I thought "Sweetums" was Lips' name, until I noticed the Sweetums name in The Muppet Movie as well, and wondered who Sweetums was. I first learned his name was Sweetums in The Frog Prince (but even then for awhile I thought maybe his name was Jack Sweetums).
At a young age I thought that Statler and Waldorf were judges, mainly because I heard my mom refer to them as judges. I don't know if she saw the Diana Ross episode and thought that was their regular job or what.
I thought that Traveling Matt (and maybe Boober) was performed by Jim Henson.
I thought that the compilation videos from Playhouse Video were full episodes, only without the opening, as opposed to videos that featured clips from the show.
When I first noticed that the credits for The Muppet Movie listed "Floyd Pepper" I thought that "Pepper" was a seperate character from Floyd (they really need to refer to Floyd''s full name more often). In my mind I thought maybe Pepper was Doglion, due to his brief line at the beginning (also, I thought Doglion's horns were devil horns).