Below is a list of enemies that have been turned into Cipherites by Bill Cipher in the game, Multiverse Umbrella. They all appear in different areas of The Cipher's Maze.
Goomba: The weakest class of Cipherites. They appear in all areas of Story Mode.
Koopa Troopa's. They appear in every world in the Story Mode, and they're the second weakest.
Stalfos. Strong for skeletons, they only appear in Desert Ruins and The Fire Temple.
Skull Kids. They only appear in The Forest Temple, Slenderman's Forest, and Termina Fields.
Motobugs. Only appearing in Mecha Sonicland and Death Egg Carrier, these things aren't that powerful.
The Pyrobot. Only appearing in Lava Mountain and Metropolis, this guy flares with fury!
Waddle Dee. Appearing in Green Greens, The Halbred, and Poke Floats, this guy is darned weak!
Rabbids. These guys can only be found in Pile To The Moon and The Rabbid Battle.
Big Daddy. Found in Don't Mess With Daddy, Big Daddy is the first general of the Cipherites.
Big Boo. Bill Cipher used Boolossous as the guard of Luigi's Mansion, and gives him the Power Of Fear.
Grunkle Stan. Turned into a Cipherite early in the game, Stan can pack a pucnh!
Turbo. Bill gave him another chance, and turned him into the King Of Racing and Games.
2007 Godzilla. Although this guy was turned into a Cipherite, he still has a mind of his own.