|I think I see a few others, but I'm not quite sure on them:
14, 07- 1 Spear Guy, 1 Medi Guy, 1 Spike Top
This formation is listed in the Jade Jungle formations. While Spear Guys are normally in that location, Medi Guys and Spike Tops are located in completely different formation groups. No other Jade Jungle formation has Medi Guy or Spike Top as extra enemies, meaning this was probably from a time where these enemies were compatible, or the Medi Guy and Spike Top overwrote the original enemies for this formation.
17, 01- 2 Petit Piranhas
Located after Lava Piranha. This formation was probably just a debug formation to test out the Petit Piranhas without having to battle Lava Piranha every time.
18, 1D- 1 Amazy Dayzee, 2 Bzzaps
18, 1E- 4 Amazy Dayzees
Not quite sure on this one. The only Amazy Dayzee formation I've seen is the one with 1 Amazy Dayzee and no other enemies, so I'm not sure if this is unused or not.
1E, 01- 1 Paragoomba, 1 Gray Magikoopa (on foot)
This one is definately unused. While most boss formations only have the boss in it's own "group" this one is located in the group reserved for the Monstar fight. What the programmers were going to use this formation for is unknown.
25, 03- 2 B. Bill Blasters, 1 Koopatrol
25, 04- 2 B. Bill Blasters, 1 Magikoopa
I'm not sure about this one either. I didn't recall any other enemies with the Bombshell Bill Blasters, but again, I'm still not sure if these are unused.
Now regarding the unused enemies:
This enemy only appears in 3 formations for the sewers, which are:
1A, 03- 1 Dark Koopa, 2 Dark Paratroopas
1A, 08- 2 Dark Paratroopas
1A, 09- 3 Dark Paratroopas
Not sure why it was scrapped, for it's entirely complete in battle.
Only one formation in the entire game has this enemy. It's listed in the very last formation in the Crystal Palace group, where only 1 appears in battle. There are quite powerful, but considering that the room after the dino's room contains a save point, maybe they changed the battle to a puzzle instead to be safe, so if the player dies in the fight, they go all the way back to the last save point, which is pretty far considering you had to beat these guys to open the next save point.