Alleged Lookalikes

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Characters who have an enigmatic connection of some kind will often be similar in other ways. Usually this means they have similar movesets, or something, but sometimes that's impractical or the writers decide they need something that people can notice without seeming goofy.

That's when the goofiest similarity of all crops up, the Alleged Lookalike. This is when the cast has difficulty telling two characters apart, or otherwise notes physical similarities between them - but to the audience, they don't look any more alike than any other pair of characters.

This only covers cases where two characters are compared in a way that to the audience is clearly not appropriate; just saying You Remind Me of X doesn't count. See also:

Non-Identical Twins, for when the subjects are supposed to be biologically identical
Easy Impersonation, for when it's a villain being mistaken for a hero

Examples of Alleged Lookalikes include:

Anime and Manga

In Cardcaptor Sakura Sonomi comments on how much Sakura looks like her mother, to the point of being surprised at the resemblance before she even knew who Sakura was. Yet there is no noticeable resemblance between them (Touya actually looks much more like their mother than Sakura does).
In Inuyasha, everyone initially compares Kagome to Kikyo. Since the series suffers from Only Six Faces and that's the only real physical similarity between the two, one might suspect everyone in the first episode or two is nearsighted.
In Yu-Gi-Oh!, no-one ever seems to see a difference between short, moe, Tareme-eyed, soft-voiced Yugi and his not-quite-so-short, bishonen, Tsurime-eyed, deep-voiced alter ego. Some fans have tried to explain the (apparently not so) obvious changes as audio-visual cues to the audience that do not actually exist in-universe. Since every once in a blue moon somebody will mention one of the changes in passing, this explanation has not been widely accepted.

Film

In Gattaca, the fact that Vincent is able to disguise himself as Jerome using his DNA samples is believable, but, looks wise, they aren't that similar. Jude Law and Ethan Hawke just don't look alike, at least not enough to confuse one for the other.
- This is handwaved in the movie as people (especially cops) being so confident in their genetic analysis material that "who looks at the face, nowadays?". The only person to notice is the Love Interest who's surprised when she meets the real Jerome.
In the very goofy 1991 movie Mystery Date, everyone confuses Ethan Hawke with Brian McNamara (playing his older brother), despite the fact that the two bear next to no resemblance to each other. Seriously. They even claim to give Ethan Hawke the same haircut, but he still has that bowlcut style haircut he had in every movie he made in the early 90s. It's ridiculous.

Live-Action TV

Happens in Kamen Rider the First, where the woman only spots one of the two Hopper operatives in night time, making it harder to distinguish their Palette Swap. On top of that, she's seen Hopper no. 1 without the helmet once, but because of aforesaid problems with color perception, she doesn't know that it him who saves her later since he keeps the helmet on this time, AND she comes across Hopper no. 2 in the daytime and thinks that's the one who saved her. This being the big-budge remake, the producers knowingly pimped out the suits with heavy detailing just to make sure they weren't mere palette swaps this time.

Video Games

In Kingdom Hearts II, the members of Organization XIII keep calling Sora "Roxas". This is... confusing, since to some degree they seem to actually believe he is Roxas, but they're also messing with his head, and it's hard to tell which is happening.

Western Animation

Family Guy: Brian is in a Spot the Imposter situation between Regular Stewie and EvilerThanUsual Clone Stewie. We can tell which is which because they have reversed color schemes on their clothes: Regular!Stewie has red overalls with a yellow shirt and ETUC!Stewie has yellow overalls with a red shirt.