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}

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.

Well, I personally think that Leta is a good character, but I am also confused by why people like her to the extent that they do. My two main issues with her are 1) she was a cause behind her brother's death, which she did feel guilty for throughout her life but that doesn't erase the action. and 2) she set a dangerous creature in Hogwarts (due to an experiment gone wrong) and allowed Newt to take the blame for her. I think this might be the reason that Queenie referred to her as a 'taker' is because instead of owning up to her actions (which she should have learned how to do by then) she allowed her only true friend to take the blame for her.

One could use her childhood and upbringing to defend her, but we can take someone like Sirius for example. Sirius was raised a certain way, and shunned by his family for being sorted in Gryffindor, his mother burning off his face from the family tree before he had even gotten out of the house. Nonetheless, he grew up to become a good person. The way someone is raised can explain their actions, but I don't think it should excuse them.

The main difference between Leta and Sirius as characters, in my opinion, is that Sirius grew as he became older and matured, while Leta pretended to, but on the inside stayed the same (kinda selfish) person. Idk though, maybe I just didn't see enough of Leta to really make a judgement.