When Metal Sonic plugs itself into a machine in Sonic Mania, it’s actually a reference to the penultimate boss of Knuckles Chaotix, where it uses a very similar mechanism.
In the original Hydrocity Zone in Sonic 3, the background tiles contained a few statues of Sonic hidden away.
With its return of the zone in Sonic Mania, and with the change back to a more Sonic-2-styled spriteset for Sonic, the statue also got a change back to a more classic style.
In Act 2 of Sonic Mania’s Press Garden Zone, the player can become frozen in a block of ice, but they won’t animate. Hidden inside the game are some unused animations where they would look around and blink.
Sonic’s Act Clear animation in Sonic Mania makes reference to one of the earliest “lost animations” from the series.
Early screenshots of Sonic 1 showed Sonic jumping in the air at the end of the round, but was not in the final game. The frames of animation were later found within the game’s data, with Sonic Mania making use of the pose.