Maybe the fast travel is super sensitive to gravity variances, and if there was a relatively large (i.e. still quite small) change to local gravity along the path of travel the safety systems would kick it out into normal space. It operates on complex gravity surveys that are not updated all that often (i.e. when a star blows up or something else pretty significant).

And, the villians have a fairly large ship / object they can move around to disrupt travel. I'd say they'd have a pretty limited supply of them, and they'd only deploy it for something quite important, and would need pretty decent intelligence on where to plop it.

So many good responses here. I think you could write the story both realistically and plausibly. In your description, the "jump drive" is just fast sub-light travel- no bending or bridging of space-time, no teleportation mechanics. They're just flying fast, like, real fast. So slow them down without destroying then in the process.

Interdiction rockets that chase down the target, attach, then counter-thrust to stop them? Deploy an advanced substance to snare them (e.g. a liquid or polymer web to brake their kinetic energy mid-flight)? Disable their thrust (e.g. with an EMP or weapon) then brake them (or match speed and mate with their craft).

I think since it's traditional sub-light travel, it's more akin to "how do I stop the train" rather than the usual sci-fi "how do I drop them out of warp" or "how do I intercept this wormhole".

@DmMacniel If they don't need to catch, only destroy, and the Jump is an on-rails sort of thing then some sort of faster-than-jump weapon would be enough. The bad guys can make jump deadly for the heroes because the guns shoot faster and once you've jumped you can't dodge.