Given the context, I interpreted Komponisto's comment as saying that to the extent that we reason correctly we are using Bayes' theorem, not that we always reason correctly.
Even if the claim is worded like that, it implies (incorrectly) that correct reasoning should not involve steps based on opaque processes that we are unable to formulate explicitly in Bayesian terms. To take an example that's especially relevant in this context, assessing people's honesty, competence, and status is often largely a matter of intuitive judgment, whose internals are as opaque to your conscious introspection as the physics calculations that your brain performs when you're throwing a ball. If you examine rigorously the justification for the nu...
"The mathematical mistakes that could be undermining justice"
The linked paper is "Avoiding Probabilistic Reasoning Fallacies in Legal Practice using Bayesian Networks" by Norman Fenton and Martin Neil. The interesting parts, IMO, begin on page 9 where they argue for using the likelihood ratio as the key piece of information for evidence, and not simply raw probabilities; page 17, where a DNA example is worked out; and page 21-25 on the key piece of evidence in the Bellfield trial, no one claiming a lost possession (nearly worthless evidence)
Related reading: Inherited Improbabilities: Transferring the Burden of Proof, on Amanda Knox.