Maya Fey qualifies. While 17-19 isn't incredibly old, you wouldn't guess she's that old based on her looks and actions; especially her actions.
Apollo Justice is 22 years old. However, in the second case of the game, the police seem to be under the impression that he's of the same age as Trucy (who's 15), shooing him away from the crime scene telling him to "go play somewhere else." Lampshaded in a playable flashback seven years before that, where you can get a picture of Apollo...who looks exactly the same at age 15 as he does at 22.
Likewise, Lamiroir's age is 40 years old according to her profile in the Court Record, despite her looking like a woman in her mid-twenties. Most likely a side-effect of being Apollo's mom.
In Narcissu, the female lead Setsumi is 22 years old, but the 20-year old male lead often comments that she looks considerably younger than him. For Setsumi, whose life consists of a hopeless cycle of hospitalization and release, "time has stood still" ever since she was first hospitalized in middle school.
Angie in Shikkoku No Sharnoth looks and acts like a little girl, but she's about the same age as the both Mary and Charlie and is the only one with an actual fiancee.
Saber is about twenty-five years old (i.e. not counting the centuries since King Arthur's death), but fifteen in appearance (when she stopped physically aging). Ilya, looking about ten years old, is actually older than Shirou (who's about seventeen).
In Fate/Zero, when Ilya is actually around eight years old, Kiritsugu is worried because her growth is so slow that she only weighs about twenty pounds!
And apart from these examples, Gilgamesh drank a youth potion in Fate/hollow ataraxia and is walking around in the form of an adorable elementary school aged version of himself.
Every single female in Kanon, Air, CLANNAD, etc. It's particularly jarring when we're supposed to believe that characters who look no older than sixteen are mothers and aunts of other characters. For example: In Clannad, Akio and Sanae Furukawa look barely older than their daughter, Nagisa. Sanae is often mistaken for Nagisa's older sister in the anime.
Emi of Katawa Shoujo is short and has a youthful appearance, but is one year older than Hisao and the rest of the girls, having taken a year off of school while relearning how to walk.
In Hatoful Boyfriend, Dr. Shuu's human-style portrait shows him as an attractive young man, but he's apparently closer in age to Ryouta's parents (for context, Ryouta's mother is dying of old age during the storyline). Somewhat justified if you consider that as a bird, his age would show differently.
Nageki Fujishiro has a zig-zagging example due to bird aging: his human-style portrait is a young-looking boy, which actually fits him as a first-year student, but his bird portrait has the iridescent throat markings and green eyelids of an adult male mourning dove. Further complicating the issue, he's been a first-year student for five years now, and his foster-brother grew up to be one of the teachers.
The protagonist's mother looks younger than he does in Dra Koi apart from her slouch and chain smoking.