We consider fundamental issues of the mathematical theory of the wave propagation in waveguides with inclusions. Analysis is performed in terms of a boundary eigenvalue problem for the Maxwell equations which is reduced to an eigenvalue problem for an operator pencil. We formulate the definition of eigenwaves and associated waves using the system of eigenvectors and associated vectors of the pencil and prove that the spectrum of normal waves forms a non-empty set of isolated points localized in a strip with at most finitely many real points.