Sonic 4 EP1 Boss Theme was actually from an early prototype of Sonic 3D Blast

Sonic 4

https://www.youtube.com/watch?v=cGOh3loQ6cM

Sonic 3D Blast 825 Prototype

https://www.youtube.com/watch?v=Te8RveELSpg

The Big Arms boss from Sonic Generations 3DS originaly used the Doomsday Zone theme instead of the Sonic 3&K Final Boss theme

The First Boss In Sonic CD is called the EGG-HVC-001.

The Last part HVC-001 is the Code name for the Famicon

Sonic's Top Speed animation from Sonic Mania is a reference to Sonic 2 Beta.

The Theme for Sunset Park Act 3 from Sonic Triple Trouble is a lower pitch version of an unused theme from Sonic Chaos