I was almost positive Bouffalant was a Tarous evo.
I once thought that Tauros was Pinsir's evolution... bear with me, as I was really young, but the reason being that Tauros directly follows Pinsir in the Pokédex, as well as them both having horns.
I thought that Zoroark evolved from Zorua... they look and act way too similar to not be related at all.
I saw this fan prediction drawn before Zoroark was revealed (he was just a silhouette). I don't remember if I saw this before or after I knew what Zoroark looked like... but this was incredibly believable. It matches the silhouette, not to mention that Lucario was quite popular so it would make sense. (I actually like his design more than the real one)
And I thought that Raichu evolved into something, due to the trader in Cinnabar lab saying, "That Raichu you traded me went and evolved!"
i used to think that Hitmonlee evolved into Hitmonchan xP (this was before their lines were officially linked with a common pre-evo though)
As well as assume that Carvanha evolved into Sharpedo, who then evolved into Garchomp :c
On the other end of the spectrum, i about flipped a gasket when i found out that Trapinch evolved into Vibrava, or that Surskit evolved into Masquerain!
I thought that Arbok evolved into Seviper waay before 4kids made the same mistake. I also thought that Eevee evolved into Espeon and Umbreon via the Sun and Moon stones.
Oh, and it took me forever to realise that Bellossom was even related to Gloom, probably had something to do with them looking nothing like one another.