When is it a solution a knee jerk reaction and when is it just a bad idea, not a knee jerk reaction?

A knee jerk reaction is about responding to something in the moment, with no thought to cause, reason, or outcome.
When someone has thought things through, and still responds in a negative way, that is considered bad judgement.

People having knee jerk reactions are not dependent on specific types of issues; more it is the manner in which a person responds to something, as @Patty_Melt has described.

…and still responds in a negative way, that is considered bad judgement. could just mean that someone disagrees with the original opinion.

Much of what Trump tweets about is knee jerk because he has no brain.

But does the expression seem to be used by people whenever their reasoning is easily refutalble?

Knee jerk responses (vs. “reactions”) are quite often easily refuted, but not always.