In Fantastic Beasts: The Crimes of Grindelwald Leta Lestrange says

to Dumbledore something like "everyone thinks I'm bad". She is also convinced Dumbledore himself believed she was bad.

Why would she say that? We do not have any evidence she acted bad at school, actually quite the opposite, despite her being in Slytherin.

We also see a girl in Dumbledore's class saying something like "I was waiting for it" when Leta got to face boggart which implies other student really didn't like her

We also see her as a pretty nice young lady in her adulthood.

She might consider herself bad because of what happened to her brother, but no one knew she was the reason for his death.

So what made people see her as a bad person in school or after if we never see her acting as one?

The Lestranges were thought ‘evil’, so they thought Leta was too.

It was very likely that people, including the students at Hogwarts, were prejudiced against Leta before they’d ever even met her because of her family name, Lestrange. When Queenie reads Newt’s mind, and heard the girl in his photo is Leta Lestrange, the first thing she says is that the family is “you know”, which likely refers to their notoriety in the wizarding world.

“QUEENIE

(reading his mind)

Leta Lestrange? I’ve heard of that family. Aren’t they kinda—you know?”
_{^{- Fantastic Beasts and Where to Find Them (The Original Screenplay)}}

This is confirmed by the executive producer of Fantastic Beasts: The Crimes of Grindelwald, who says that Leta is burdened by her family name, and her being a Lestrange makes people assume she’s a bad person because of the family’s reputation.

But according to executive producer David Heyman, Leta might simply be misunderstood. “Leta is in some ways burdened by her name,” he says. “The fact that she is a Lestrange has led some people to believe her to be a bad person. But as with a lot of J.K. Rowling’s writing, you have a rich complex character, and it’s one that Zoe brings to life.”
_{^{- Zoë Kravitz reacts to her character getting dissed in Fantastic Beasts (Entertainment Weekly)}}

Zoe Kravitz also mentions that the reason Leta is ‘edgy’ is because she’s used to being judged.

And from what I hear, she’s got a bad reputation?

Yeah, being a pureblood is a big deal. When she walks into a party people take a double take. She’s always felt like an outcast because of that and she’s very edgy because she’s used to being judged, and has created a bubble of protection of herself.
_{^{- Zoë Kravitz reacts to her character getting dissed in Fantastic Beasts (Entertainment Weekly)}}

One of the girls mocking Leta says how the name Lestrange makes her feel sick, implying that it’s a problem with the family that’s extended to Leta because she’s part of it.

GRYFFINDOR GIRL 2

I don’t blame them, she’s so annoying. Even the name Lestrange makes me feel sick—

LETA flings herself into their path, pointing her wand.

13-YEAR-OLD LETA

Oscausi!
_{^{- Fantastic Beasts and Where to Find Them (The Original Screenplay)}}

Grindelwald also mentioned her being despised among wizards.

GRINDELWALD

Leta Lestrange . . . despised entirely amongst wizards . . . unloved, mistreated . . . yet brave. So very brave.
_{^{- Fantastic Beasts: The Crimes of Grindelwald (The Original Screenplay)}}

So, it seems highly likely that people’s problems with Leta stemmed mainly from her family name.

Leta had too much emotional baggage to become a model student and alter the prejudices against her

As Bella's answer mentions, the Lestrange family is infamous and Leta was eyed with suspicion and distrust at Hogwarts - not the best conditions to make friends and become popular in the wizarding community.

One could argue that Leta wasn't the only student who arrived with unwanted baggage to school and who had to endure the consequences for the actions of her family members: for one, there was Albus Dumbledore, whose father, Percival was sentenced to life at Azkaban for slaughtering three muggle boys. But while Albus did everything to overcome the prejudices against his family and prove them wrong, it seems Leta agreed with her accusers about her family and her own character.

In addition as a girl, Leta wasn't taken seriously by her father, the patriarch of the Lestrange family:

LETA: My father owned a very strange family tree. It only recorded the
men . . . We glimpse a tree with an orchid-like flower twisting around
it.

she wasn't even loved:

LETA: Say it . . .

KAMA . . . he never loved you.

add to this the unfortunate and melodramatic story of losing her brother at sea, and we got Leta, a bright witch, distrustful of authority figures, with a gloomy disposition, defensive and sullen, burdened with self-hatred and in general unapproachable. Not the best recipe to become the sunshine of the school. She characterises herself as a monster:

NEWT You didn’t mean to do it, Leta.
So it wasn’t your fault.

LETA
Oh Newt. You never met a monster you couldn’t love.

She despised herself and idealised Newt, who is basically the wizard equivalent of
Francis of Assisi, so it's no wonder that she wasn't able to win over people and remained unpopular in her community.

Because she repeatedly jinxed her fellow students who she doesn’t like, and they don’t like her. The way it’s worded is as if they didn’t like her first mind you probably because of who her family is as is mentioned below.

SCENE 67

INT. EMPTY HOGWARTS CLASSROOM—SEVENTEEN YEARS PREVIOUSLY—MORNING

13-YEAR-OLD LETA stands hiding inside the empty classroom while students in cloaks trundle by, pushing trunks and carrying owls. It is the last day of the winter term and nearly everyone is going home.

ANGLE ON TWO 13-YEAR-OLD GRYFFINDOR GIRLS pushing trunks.

GRYFFINDOR GIRL 1 You know she stays here every vacation. Her family don’t actually want her home.

GRYFFINDOR GIRL 2 I don’t blame them, she’s so annoying. Even the name Lestrange makes me feel sick—

LETA flings herself into their path, pointing her wand.

13-YEAR-OLD LETA Oscausi!

GRYFFINDOR GIRL 2’S mouth is sealed shut as though she never had one. Triumphant, LETA flees the scene, pushing past shocked students.

GRYFFINDOR GIRL 1 (screams) Professor McGonagall! LESTRANGE HAS DONE IT AGAIN!

MCGONAGALL (O.S.) Lestrange, stop running! LESTRANGE! Disobedient children. Stop! Shame on the House of Slytherin. One hundred points! Two hundred! Get back here, right now! Stop! Stop it! Stop it! You stop it! Get back here!

_{Fantastic Beasts: The Crimes of Grindelwald - The Official Screenplay}