When disguised as ex-Auror Mad-Eye Moody in The Goblet of Fire, Barty Crouch Jr. fooled many, including the true reason he disliked Draco Malfoy.

When they meet in Harry Potter and the Goblet of Fire, Barty Crouch Jr. despises Draco Malfoy for good reason. Voldemort hires Barty Crouch Jr. to infiltrate Hogwarts in order to get closer to Harry Potter in the fourth Harry Potter film.
He accomplishes this by assuming the identity of ex-Auror Alastor “Mad-Eye” Moody and assuming the position of professor of Defense Against the Dark Arts. Crouch, disguised as Moody, attacks Draco by transforming him into a ferret.
At first glance, this appears to be a gesture of goodwill, as “Moody” claims he did it because Draco was planning to curse Harry behind Harry’s back. This kind of minor detail in Goblet of Fire conceals the twist that Moody is actually Crouch in disguise.
However, when looking back on the scene and realizing that it was Crouch who did it and was reveling in Draco’s misery, “Moody” attacking Draco takes on a whole new meaning. Attacking Draco and using it as a teaching opportunity was merely a cover for his true motivations.
Explained: Barty Crouch Jr.’s Malfoy Dislike

When discussing Durmstrang’s Headmaster and former Death Eater Igor Karkaroff in the Goblet of Fire book, “Moody” tells Harry, “If there’s one thing I hate more than anything else, it’s a Death Eater who walked free.” This implies that the ex-Auror is still enraged that these dark wizards were able to get away with their evil deeds.
Crouch later asks Harry if Voldemort punished the Death Eaters who escaped Azkaban after Harry defeats Voldemort in the graveyard. Crouch repeats the line, now specifying that he despises any Death Eater who denied Voldemort and did not remain loyal after Voldemort vanished.
His hatred for Death Eaters stems from being imprisoned in Azkaban for years for his service to Voldemort while others, such as Lucius, walked free.
Lucius Malfoy was one of many Death Eaters who refused to swear allegiance to Voldemort after the end of the First Wizarding War and thus represents the type of person Barty Crouch Jr. despises the most.
Draco becomes the target of all of Barty Crouch Jr.’s rage because Lucius Malfoy is not present at Hogwarts, but his child is, just as Severus Snape hated James Potter and took it out on Harry.
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How Lucius Malfoy Escaped (Despite Being A Death Eater)

As Voldemort’s second-in-command during the First Wizarding War, Lucius Malfoy had some brutal moments as a Death Eater.
Because Lucius was a known Death Eater when Voldemort vanished, he was summoned to account for his crimes. Lucius used a combination of blackmail, bribes, and flattery to get many Ministry workers in his pocket before his trial in order to save his social standing and reputation.
When Lucius was brought to trial in the Court of Magical Law, he claimed to be under the influence of the Imperius Curse, a spell that takes control of other people’s will. He was believed and set free because he had control over many Ministry of Magic members.
In the books, Barty Crouch Jr.’s hatred for Draco is unjustified, but his reasons are also hypocritical. In the Goblet of Fire book, a flashback shows Barty Crouch Jr. being sent to Azkaban while denying his involvement.
The film Harry Potter and the Goblet of Fire alters this by having Barty Crouch Jr. never deny his loyalty, strengthening his hatred for Death Eaters who abandoned Voldemort and making his hatred of Draco all the more disturbing.
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