Yes, I was one of the people who thought Alomomola would be an evolution of Luvdisc, but I also believed that Emolga would be an evolution of Pachirisu. In fact, I was almost sure of it.
I also used to think Cloyster evolved into Gastly, as that 'pearl' in Cloyster looks just like Gastly, and plus they're right next to each other in the Nat Dex.
When I started playing Pokemon and saw Mew and Mewtwo for the first time, I thought Mewtwo evolved from Mew, so it always puzzled me that Mew was no 151 and Mewtwo no 150.
So my mistakes through the ages:
-Farfetch'd evolves to Doduo;
-Plusle and Minun are linked to Pikachu in some way;
-Skarmory is something like a new legendary bird;
-Latios and Latias are related to Lugia in some way;
-Blue Shellos is the Lapras baby;
-Alomomola is Luvdisc evolution;
-Deerling is the Stantler baby;
-Bouffalant isn't Tauros evolution but is related to Tauros and Miltank (for example they could have a common baby such as Tyrogue);
When Gen II first came out, I thought Remoraid evolved into Mantine, since in the second Pokemon Stadium game for Nintendo 64, Mantine is shown with a Remoraid under its fin.
And in the original games, I thought that the Dratini line ended with Gyrados instead of Dragonite, because I couldn't imagine Magikarp ever being useful at that time XD
I used to think Poochyena had a 3 stage evolution line
Poochyena - Mightyena - Absol
They look similar anyways...
"Octillery from Remoraid? What?" (me, eleven years ago)
Also, for a long time I thought Slowking was a Slowbro evolution, instead of a parallel Slowpoke evo.
Ah, and back in my earliest memories about Pokémon, in 1998-99, I heard Pikachu had an evolution called "aichu" or "raichu" or "(random letter)aichu", but I'd never seen one at that point. My cousin got a Pokémon toy and I got excited because I thought it was that "enigmatic" Pikachu's evolution... actually it was Eevee.
Ah, and at some point I ate the Pikablu hoax, as a Raichu evo.
I thought Magcargo might evolve into Torkoal. And I remember that some people theorised that Gligar would evolve into Drapion before D/P were released.
I thought Shellos would evolve into Lapras who would evolve in Gastrodon.
I totally thought that Plusle and Minun had something to do with the Pikachu line, perhaps alternate evolutions for Pichu. Also thought that Latias and Latios had to be related to Lugia, and Pachirisu evolved into Emolga. And add me to the Luvdisc -> Alomomola list.. still hoping for a connecting middle stage.
When Marill first came out, there was this confusion that Marill was named "Pika-Blue", and that Pikachu evolves into Marill if given a Water Stone or something. I, of course, was one of the innocent victims who tried to get a Marill in that way.
There was this rumor that Articuno evolved into Lugia, and Moltres evolved into Ho-oh. I didn't believe that, though.
For the longest time, I thought that Slowking evolved from Slowbro. *facepalm* I think that's about it, though.
I use to think pinser evolved into heracross