Variational principles for symmetric complex scattering matrices (e.g., the S matrix or the T matrix) based on the Kohn variational principle have been thought to be free from anomalous singularities. We demonstrate that singularities do exist for these variational principles by considering single and multichannel model problems based on exponential interaction potentials. The singularities are found by considering simultaneous variations in two nonlinear parameters in the variational calculation (e.g., the energy and the cutoff function for the irregular continuum functions). The singularities are found when the cutoff function for the irregular continuum functions extends over a range of the radial coordinate where the square-integrable basis set does not have sufficient flexibility. Effects of these singularities generally should not appear in applications of the complex Kohn method where a fixed variational basis set is considered and only the energy is varied.