(Guide based on content provided by The Cutting Room Floor)
Source: TCRF

There are a number of oddly placed objects throughout the game, many of which you never see in gameplay, or even Debug Mode. I won't go into too much detail on why each object may have been placed as shown. You can visit the TCRF link for more on that.

GHZ1

In Green Hill Zone Act 1, a Motobug is suspended above an abyss near the first group of spikes on the lower route. It is quickly erased from memory because there are no collision tiles for it to latch onto, which it looks for immediately upon spawning.

GHZ2

Green Hill Zone Act 2 has multiple misplaced enemies, such as a Crabmeat under the section with the moving pillars and spikes just before the checkpoint. They cannot be seen in gameplay for the same reason as the GHZ1 Motobug.

GHZ3

A purple rock can be found below the boundaries of the map in Green Hill Zone Act 3, near the boss fight. It is impossible to reach it without the use of debug mode. You can also find a Buzz Bomber that is impossible to reach at coordinates 21B0,0000.

LZ1

In Labyrinth Zone Act 1, there is a group of spikes buried in 12D3,0675. It is impossible to see them because they are out of bounds and the foreground tiles are in a layer above the sprites.