These have been floating around the Internet for a while, but I figured I'd share them here. It's believed that due to programming errors, or not being able to implement things like holdable items that Game Freak changed evolutions around. It's been deemed programming errors, or just oversights. Keep in mind these are just theories and I may not agree with some of them, but there are a few which may leave you scratching your head.
Venonat-> Butterfree
--Mouth matches up and seems more plausible--
Caterpie-> Metapod -> Venomoth
--Metapods slender body seems to fit Venomoth better--
Magikarp -> Dragonite
--Similar color, and has a similar underbelly
Dratini -> Dragonair -> Gyarados
--Color scheme stays the same, height and weight increase proportionally. Gyarados is a sea serpent similar to how Dragonair looks. Red Gyarados is later explained in Generation II as a cover-up--
That's where people normally draw the line with these but there's one more that I've thought up.
Togepi as Chansey's child form
-Chansey originally referred to as 'Lucky' in the Red and Blue Beta. Togepi's hidden ability is 'Super Luck' which seems like a stretch. However Togepi is one of the first Pokemon to be introduced to Generation II which brings up the idea that Pokemon eggs were planned for Generation I and couldn't be worked into the game so Togepi was scrapped altogether in place of Happiny in Generation II. Less plausible, but I think Togepi was a special Pokemon that was relevant in the anime. So this one is a bit offbeat and probably not true.
Venonat-> Butterfree
--Mouth matches up and seems more plausible--
Caterpie-> Metapod -> Venomoth
--Metapods slender body seems to fit Venomoth better--
Magikarp -> Dragonite
--Similar color, and has a similar underbelly
Dratini -> Dragonair -> Gyarados
--Color scheme stays the same, height and weight increase proportionally. Gyarados is a sea serpent similar to how Dragonair looks. Red Gyarados is later explained in Generation II as a cover-up--
That's where people normally draw the line with these but there's one more that I've thought up.
Togepi as Chansey's child form
-Chansey originally referred to as 'Lucky' in the Red and Blue Beta. Togepi's hidden ability is 'Super Luck' which seems like a stretch. However Togepi is one of the first Pokemon to be introduced to Generation II which brings up the idea that Pokemon eggs were planned for Generation I and couldn't be worked into the game so Togepi was scrapped altogether in place of Happiny in Generation II. Less plausible, but I think Togepi was a special Pokemon that was relevant in the anime. So this one is a bit offbeat and probably not true.