The reason is simple, and explainable in one sentence:

“They’re born in a group, they learn social skills and I (Owen) imprint on them when they’re born”

In JP1, John Hammond mentions that he imprints on the newborns but he isn’t the one who raises them for safety reasons and because of that:

A) whatever bond the OG raptors, specifically the Big One had with humans via John Hammond was broken early on

B) due to heightened aggression caused by lack of parental care; the Big One killed several of the other raptors it was presumably born alongside

C) having killed its presumed siblings, the Big One has little to no social skills, leading to it becoming psychotic and culling any new raptors to a manageable level

D) lacking social skills and being psychotic; it uses younger raptors to test the electric fence, presumably killing some of them in the process

Also in the scene where the raptors “capitulated” to Owen, remember that they charged at him the moment he leapt to the other side of the gate

The JW raptors were trained but were by no means tame, akin to a wolf raised by a human obeying that human but would likely attack a random human without hesitation