When you get to the boss at the end of Hydrocity Act 1, it plays the Dr. Robotnik music rather than the mini-boss music. (This goof was fixed for "Sonic 3 & Knuckles".)
When the countdown begins to notify the player that Sonic is running out of air in Hydrocity Zone when fighting the mini-boss, if Sonic replenishes his air, the music will switch to the mini-boss music from "Sonic & Knuckles". This also happens during the fight with Robotnik in the same Zone.
If Sonic is sucked up by Robotnik's propeller in the Hydrocity Zone while being Super Sonic, his sprite will change back to the regular Sonic sprite while still retaining his Super Sonic abilities and will also not lose any rings. He will remain this way until the level ends. This was fixed in "Sonic 3 & Knuckles".