The Chebyshev tau method is examined; a numerical technique which in recent years has been successfully applied to many hydrodynamic stability problems. The orthogonality of Chebyshev functions is used to rewrite the differential equations as a generalized eigenvalue problem. Although a very efficient technique, the occurrence of spurious eigenvalues, which are not always easy to identify, may lead one to believe that a system is unstable when it is not. Thus, the elimination of spurious eigenvalues is of great importance. Boundary conditions are included as rows in the matrices of the generalized eigenvalue problem and these have been observed to be one cause of spurious eigenvalues. Removing boundary condition rows can be difficult. This problem is addressed here, in application to the Bénard convection problem, and to the Orr-Sommerfeld equation which describes parallel flow. The procedure given here can be applied to a wide range of hydrodynamic stability problems.