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$\mathcal{PT}$ symmetry is a unique platform for light manipulation and versatile use in unidirectional invisibility, lasing, sensing, etc. Broken and unbroken $\mathcal{PT}$-symmetric states in non-Hermitian open systems are described by scattering matrices. A multilayer structure, as a simplest example of the open system, has no certain definition of the scattering matrix, since the output ports can be permuted. The uncertainty in definition of the exceptional points bordering $\mathcal{PT}$-symmetric and $\mathcal{PT}$-symmetry-broken states poses an important problem, because the exceptional points are indispensable in applications as sensing and mode discrimination. Here we derive the proper scattering matrix from the unambiguous relation between the $\mathcal{PT}$-symmetric Hamiltonian and scattering matrix. We reveal that the exceptional points of the scattering matrix with permuted output ports are not related to the $\mathcal{PT}$ symmetry breaking. Nevertheless, they can be employed for finding a lasing onset as demonstrated in our time-domain calculations and scattering-matrix pole analysis. Our results are important for various applications of the non-Hermitian systems including encircling exceptional points, coherent perfect absorption, $\mathcal{PT}$-symmetric plasmonics, etc.