When it comes to partial differential equations in physics, non-uniqueness of solutions seems to be the norm, rather than the exception. Another example would be in electrodynamics, where you get unphysical solutions to the Maxwell equations by using the advanced Green's functions, rather than the retarded ones.
In the case of the Navier-Stokes equation, this problem is worse because the equations are non-linear. In fact, the question of whether the Navier-Stokes equation always has "nice" solutions is still unsolved, and one of the millenium problems with a million dollar prize on it.
If you look at the derivation of Navier-Stokes, there is no real reason to expect any different. One usually proceeds by taking a volume of fluid and applying Newton's laws. By taking a limiting procedure one then obtains a partial differential equation. All this proves is that fluids obey the Navier-Stokes equation. Nowhere in this kind of argument does it say that every solution has to be physically relevant.
Regarding the geometric parameters you mention, the Reynolds number is one of them, although you can construct others, depending on the relevant physical scales in the system.