Two models rarely disagree at random. They disagree where the input is ambiguous, where instructions conflict, or where one model has memorized a pattern and the other has not. Label Studio's guidance on inter-annotator agreement makes the point directly: the items annotators split on are usually the same ones models find hardest, and low agreement points to ambiguous guidelines rather than careless workers (Label Studio). The same logic holds across machines. A disagreement marks an input whose correct answer is not well defined by your current specification.
That reframes the engineering problem. You are not trying to make two models agree. You are trying to find out which model is right on which kind of input, and where neither is worth trusting. The disagreement set is the cheapest place to ask that question, because it is small and it is already sorted by difficulty.
One caveat from research on agreement measurement: chance-corrected metrics like Cohen's kappa and Fleiss' kappa exist because raw agreement overstates reliability, especially when one class dominates (FiftyOne glossary). The same bias hits model agreement. If 90 percent of your inputs are class A, the two models will agree 90 percent of the time on a useless baseline. Measure agreement against that baseline, not against zero.



