For NS equations, they are trying to model something that is discrete (i.e molecules colliding) in a continuous manner. You can easily think of a condition where they fail - imagine a vaccum where there is sufficient space between air molecules, so that collisions aren't always possible. NS won't be able to predict the state of the fluid in every single point in space.
In practice, when you do CFD, no package uses direct differential simulation of NS equations, you usually have simpler approximations that are good enough for the space you are working for. And if you want accuracy, you usually do something like LBM which simulates particle collisions using probability distributions.