I'm sure there's more than one, but for me this one really stands. Kramer lives across the hall from Jerry, yet there apartments are on the same side of the building. When someone knocks on Kramer's door in the middle of the night we see a cut away to the building exterior, and sure enough a light comes on from Kramer's apartment, which is right next door to Jerry's.
The chicken roaster episode through this MC Escher architecture right into the Twilight Zone. Jerry and the K-man switched apartments because of the bright red chicken roaster sign was shining through Kramer's window and keeping him up. I've tried to sketch this out in my mind, it just doesn't add up.
In the early episodes the exterior shots of the windows didn't even match the interior shots. They're were clearly small sectional windows in the frame on the outside, but on the inside it looked completely different.
Another paradox is Jerry's bedroom. In early episodes he seemed to live in a studio apartment, his parents slept on the fold-out bed in season one, while he slept over at Kramer's that night. In later seasons a one-bedroom all of a sudden appears back in the little hallway where the bicycle hangs.
Wouldn't it be nice if reality were this malleable?