Well, it's a related, but different thing here. Usually, when you have two non-commuting observables, you can't measure both of them, so the fact that they cannot both have well-defined values due to their non-commutativity, doesn't cause any problems. Think of the SG experiment, where you can align the detector only along one axis, which makes it impossible to measure the spin along another axis at the same time. QM also doesn't assign probabilities to such joint observations of incompatible observables.
However, Isham discusses a situation where you make measurements of incompatible observables at different times. Since they are incompatible, they can't in general both have well-defined values. However, it's perfectly possible to measure incompatible observables one after another and obtain these values. In this case, QM does assign probabilities to this joint observation and this is where a counterexample to the classical behavior of conditional probabilities can be constructed.